Updated per review comments.

src/EFCore/Metadata/Builders/CollectionCollectionBuilder.cs

@@ -4,6 +4,7 @@
 using System;
 using System.ComponentModel;
 using JetBrains.Annotations;
+using Microsoft.EntityFrameworkCore.Diagnostics;
 using Microsoft.EntityFrameworkCore.Infrastructure;
 using Microsoft.EntityFrameworkCore.Metadata.Internal;
 using Microsoft.EntityFrameworkCore.Utilities;
@@ -94,13 +95,19 @@ public virtual EntityTypeBuilder UsingEntity(
             [NotNull] Func<EntityTypeBuilder, ReferenceCollectionBuilder> configureRight,
             [NotNull] Func<EntityTypeBuilder, ReferenceCollectionBuilder> configureLeft)
         {
+            if (((Model)LeftEntityType.Model).IsShared(joinEntity))
+            {
+                throw new InvalidOperationException(
+                    CoreStrings.DoNotUseUsingEntityOnSharedClrType(joinEntity.GetType().Name));
+            }
+
             var existingAssociationEntityType = (EntityType)
                 (LeftNavigation.ForeignKey?.DeclaringEntityType
                     ?? RightNavigation.ForeignKey?.DeclaringEntityType);
             if (existingAssociationEntityType != null)
             {
                 ModelBuilder.RemoveAssociationEntityIfAutomaticallyCreated(
-                    existingAssociationEntityType, false, ConfigurationSource.Explicit);
+                    existingAssociationEntityType, removeSkipNavigations: false, ConfigurationSource.Explicit);
             }
 
             var entityTypeBuilder = new EntityTypeBuilder(

src/EFCore/Metadata/Builders/CollectionCollectionBuilder`.cs

@@ -3,6 +3,7 @@
 
 using System;
 using JetBrains.Annotations;
+using Microsoft.EntityFrameworkCore.Diagnostics;
 using Microsoft.EntityFrameworkCore.Infrastructure;
 using Microsoft.EntityFrameworkCore.Metadata.Internal;
 
@@ -51,13 +52,19 @@ public virtual EntityTypeBuilder<TAssociationEntity> UsingEntity<TAssociationEnt
             [NotNull] Func<EntityTypeBuilder<TAssociationEntity>, ReferenceCollectionBuilder<TRightEntity, TAssociationEntity>> configureLeft)
             where TAssociationEntity : class
         {
+            if (((Model)LeftEntityType.Model).IsShared(typeof(TAssociationEntity)))
+            {
+                throw new InvalidOperationException(
+                    CoreStrings.DoNotUseUsingEntityOnSharedClrType(typeof(TAssociationEntity).Name));
+            }
+
             var existingAssociationEntityType = (EntityType)
                 (LeftNavigation.ForeignKey?.DeclaringEntityType
                     ?? RightNavigation.ForeignKey?.DeclaringEntityType);
             if (existingAssociationEntityType != null)
             {
                 ModelBuilder.RemoveAssociationEntityIfAutomaticallyCreated(
-                    existingAssociationEntityType, false, ConfigurationSource.Explicit);
+                    existingAssociationEntityType, removeSkipNavigations: false, ConfigurationSource.Explicit);
             }
 
             var entityTypeBuilder = new EntityTypeBuilder<TAssociationEntity>(

src/EFCore/Metadata/Builders/CollectionNavigationBuilder.cs

@@ -205,11 +205,17 @@ public virtual CollectionCollectionBuilder WithMany([NotNull] string navigationN
             }
 
             var leftName = Builder?.Metadata.PrincipalToDependent.Name;
-            return new CollectionCollectionBuilder(
-                           RelatedEntityType,
-                           DeclaringEntityType,
-                           WithLeftManyNavigation(navigationName),
-                           WithRightManyNavigation(navigationName, leftName));
+            var collectionCollectionBuilder =
+                new CollectionCollectionBuilder(
+                    RelatedEntityType,
+                    DeclaringEntityType,
+                    WithLeftManyNavigation(navigationName),
+                    WithRightManyNavigation(navigationName, leftName));
+
+            collectionCollectionBuilder.LeftNavigation
+                .SetInverse(collectionCollectionBuilder.RightNavigation);
+
+            return collectionCollectionBuilder;
         }
 
         /// <summary>

src/EFCore/Metadata/Builders/CollectionNavigationBuilder`.cs

@@ -95,11 +95,17 @@ public virtual ReferenceCollectionBuilder<TEntity, TRelatedEntity> WithOne(
         public new virtual CollectionCollectionBuilder<TRelatedEntity, TEntity> WithMany([NotNull] string navigationName)
         {
             var leftName = Builder?.Metadata.PrincipalToDependent.Name;
-            return new CollectionCollectionBuilder<TRelatedEntity, TEntity>(
-                           RelatedEntityType,
-                           DeclaringEntityType,
-                           WithLeftManyNavigation(navigationName),
-                           WithRightManyNavigation(navigationName, leftName));
+            var collectionCollectionBuilder =
+                new CollectionCollectionBuilder<TRelatedEntity, TEntity>(
+                    RelatedEntityType,
+                    DeclaringEntityType,
+                    WithLeftManyNavigation(navigationName),
+                    WithRightManyNavigation(navigationName, leftName));
+
+            collectionCollectionBuilder.LeftNavigation
+                .SetInverse(collectionCollectionBuilder.RightNavigation);
+
+            return collectionCollectionBuilder;
         }
 
         /// <summary>
@@ -126,11 +132,17 @@ public virtual CollectionCollectionBuilder<TRelatedEntity, TEntity> WithMany(
             }
 
             var leftName = Builder?.Metadata.PrincipalToDependent.Name;
-            return new CollectionCollectionBuilder<TRelatedEntity, TEntity>(
-                           RelatedEntityType,
-                           DeclaringEntityType,
-                           WithLeftManyNavigation(navigationExpression.GetMemberAccess()),
-                           WithRightManyNavigation(navigationExpression.GetMemberAccess(), leftName));
+            var collectionCollectionBuilder =
+                new CollectionCollectionBuilder<TRelatedEntity, TEntity>(
+                    RelatedEntityType,
+                    DeclaringEntityType,
+                    WithLeftManyNavigation(navigationExpression.GetMemberAccess()),
+                    WithRightManyNavigation(navigationExpression.GetMemberAccess(), leftName));
+
+            collectionCollectionBuilder.LeftNavigation
+                .SetInverse(collectionCollectionBuilder.RightNavigation);
+
+            return collectionCollectionBuilder;
         }
     }
 }

src/EFCore/Metadata/Conventions/BackingFieldConvention.cs

@@ -81,7 +81,7 @@ private FieldInfo GetFieldToSet(IConventionPropertyBase propertyBase)
             if (propertyBase == null
                 || !ConfigurationSource.Convention.Overrides(propertyBase.GetFieldInfoConfigurationSource())
                 || propertyBase.IsIndexerProperty()
-                || (propertyBase.PropertyInfo == null && propertyBase.FieldInfo == null))
+                || propertyBase.IsShadowProperty())
             {
                 return null;
             }

src/EFCore/Metadata/Conventions/Infrastructure/ProviderConventionSetBuilder.cs

@@ -200,7 +200,7 @@ public virtual ConventionSet CreateConventionSet()
 
             conventionSet.NavigationRemovedConventions.Add(relationshipDiscoveryConvention);
 
-            conventionSet.SkipNavigationAddedConventions.Add(new ManyToManyConvention(Dependencies));
+            conventionSet.SkipNavigationAddedConventions.Add(new ManyToManyAssociationEntityTypeConvention(Dependencies));
 
             conventionSet.IndexAddedConventions.Add(foreignKeyIndexConvention);
 

src/EFCore/Metadata/Conventions/ManyToManyConvention.cs → src/EFCore/Metadata/Conventions/ManyToManyAssociationEntityTypeConvention.cs

@@ -13,16 +13,15 @@ namespace Microsoft.EntityFrameworkCore.Metadata.Conventions
     /// <summary>
     ///     A convention which looks for matching skip navigations and automatically creates
     ///     a many-to-many association entity with suitable foreign keys, sets the two
-    ///     matching skip navigations to use those foreign keys and makes them inverses of
-    ///     one another.
+    ///     matching skip navigations to use those foreign keys.
     /// </summary>
-    public class ManyToManyConvention : ISkipNavigationAddedConvention
+    public class ManyToManyAssociationEntityTypeConvention : ISkipNavigationAddedConvention
     {
         /// <summary>
-        ///     Creates a new instance of <see cref="ManyToManyConvention" />.
+        ///     Creates a new instance of <see cref="ManyToManyAssociationEntityTypeConvention" />.
         /// </summary>
         /// <param name="dependencies"> Parameter object containing dependencies for this convention. </param>
-        public ManyToManyConvention([NotNull] ProviderConventionSetBuilderDependencies dependencies)
+        public ManyToManyAssociationEntityTypeConvention([NotNull] ProviderConventionSetBuilderDependencies dependencies)
         {
             Dependencies = dependencies;
         }
@@ -41,8 +40,8 @@ public virtual void ProcessSkipNavigationAdded(
             IConventionSkipNavigationBuilder skipNavigationBuilder,
             IConventionContext<IConventionSkipNavigationBuilder> context)
         {
-            Check.NotNull(skipNavigationBuilder, "skipNavigationBuilder");
-            Check.NotNull(context, "context");
+            Check.NotNull(skipNavigationBuilder, nameof(skipNavigationBuilder));
+            Check.NotNull(context, nameof(context));
 
             var skipNavigation = skipNavigationBuilder.Metadata;
             if (skipNavigation.ForeignKey != null
@@ -55,13 +54,10 @@ public virtual void ProcessSkipNavigationAdded(
                 return;
             }
 
-            var matchingSkipNavigation = skipNavigation.TargetEntityType
-                .GetSkipNavigations()
-                .FirstOrDefault(sn => sn.TargetEntityType == skipNavigation.DeclaringEntityType);
-
-            if (matchingSkipNavigation == null
-                || matchingSkipNavigation.ForeignKey != null
-                || !matchingSkipNavigation.IsCollection)
+            var inverseSkipNavigation = skipNavigation.Inverse;
+            if (inverseSkipNavigation == null
+                || inverseSkipNavigation.ForeignKey != null
+                || !inverseSkipNavigation.IsCollection)
             {
                 // do not create an automatic many-to-many association entity type if
                 // the matching skip navigation is already "in use" (i.e.
@@ -70,9 +66,9 @@ public virtual void ProcessSkipNavigationAdded(
             }
 
             var model = (Model)skipNavigation.DeclaringEntityType.Model;
-            model.Builder.AssociationEntity(
+            model.Builder.HasAutomaticAssociationEntity(
                 (SkipNavigation)skipNavigation,
-                (SkipNavigation)matchingSkipNavigation,
+                (SkipNavigation)inverseSkipNavigation,
                 ConfigurationSource.Convention);
         }
     }