All helper and solution files live in the root directory of the container, along with any tests you create.
If solution code, student code, or your helper files are nested in directories, than that directory structure will be preserved when you upload. So you won't need to change any imports when uploading code that works locally.
Here's an example file structure:
main.sh
solution.py
solutionUtils/
foo.py
bar.py
helper.py
helpers/
helper1.py
helper2.py
helper3.py
test1.sh
test2.sh