I just import class from .py in notebook and then use it:

from folder.file_folder.file_name import class

in notebook I initiate class.

I have everything in repos (notebook, py files). I have repo opened in Visual Studio and I can edit there notebooks as well. I haven't tested other IDE but it is just git repo with notebook so you can edit as well in PyCharm. Than in job you can set just notebook so it will be much easier.