Help with modules and subfolders

My project is starting to have a lot of classes, and I’d like to
organize
them.
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
really
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
the
classes there, but I don’t know if it will still work the same way it
used
to.

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,
Rodrigo

Can anyone help me with that please?