See the TEMPLATE folder for an example file structure:
00-include - folder for auxilary files (class, etc.)
01-prep - folder for sections of the preparation
02-eval - folder for sections of the evaluation
data - folder for measurement report and other data
fig - folder for figures/images/plots
script - folder for evaluation scripts
tab - folder for tables/measurement data
lit.bib - bibliography file for \citations
main.tex - the main lab report tex file
main.pdf - the lab report in pdf format
The individual files in eval/ and prep/ are intended to be numbered 1.tex, 2.tex, ...
In this format they are automatically input in the main tex file.
You can use custom file names, but will have to add the corresponding files manually in main.tex