Let's see your questions:

what is the direct bonus for the group owners?

The "bonus" word meant "payment" in that message to avoid the less repeat of this term.

And the percentage you enter in Payment then applies to all processed payments made on the website?

All site payments are coming through the Payment module, not separately via every module. This app counts the seller's income (for 1 month by default) and applies the percentage setup by admin.

Where do I actually see the income of the individual groups

There is no such possibility.