For anyone in a similar situation on future projects, i found his solution:
I made a new Take in each of the .C4D files named Alpha Mattes.
I then set the following render path:
../$take/$prj/$userpass/$userpass
This wll make the following folder structure: Alpha Mattes/Project Name/Object Buffer Name/Object Buffer Name
I found this approach useful, as I need to pass the fils onto anoher user who was not familiar with C4D, but needed to add the files to a render queue to work on them in post.
Best to get the suitable file paths set up first though so you don't need to open a bunch of files to add the new Take anfr change all the render settings.
