I don't know if this is possible... but we are wanting to create two sections of the website that both have downloads. However one section of the site will exclusively be free downloads, and the other section of the site will paid downloads.

Is this possible?

You can’t have two equal apps installed. You can allow only specific groups to submit paid files. That’s a per-group configuration. 

Can we limit paid files only to specific categories at least?

Nope.

On 11/22/2020 at 6:25 AM, Bluedrake42 said:

Can we limit paid files only to specific categories at least?

I thought about how nice this would be also.
More specifically I would like to limit member groups access to download from only some specific categories.

3 minutes ago, SJ77 said:

More specifically I would like to limit member groups access to download from only some specific categories.

You can do that by removing the permission from the specific group in the category. 

1 minute ago, Adriano Faria said:

You can do that by removing the permission from the specific group in the category. 

Ok yeah, that's a good idea