Help with modules and subfolders

My project is starting to have a lot of classes, and I’d like to
I have mainly 3 mini websites within my project, one for companies (that
will sell something), one for users (that will buy), and one for admin.

I can imagine 2 ways of organizing it: include (or require, I don’t
know what to use in this case) each group into a module, that way I’d
have 3
modules, companies, users and admin; or just create subfolders and puts
classes there, but I don’t know if it will still work the same way it

So I’d like some help to find out what is the best way to organize my
project. Cause If I don’t do anything, all the controllers (for example)
will just be there in the controllers folder.

Thank you,

Can anyone help me with that please?