Does my commission come from the full 2.5% fee or whatever?
No. The real world of credit card processing has a variety of Interchange Rates -- which is what Visa, MasterCard, etc. charge. That's their profit. Our partners usually quote 'Interchange Plus', which might be 1.5% Interchange, plus 0.5% for the processing company servicing the account. Our commission comes out of the "plus" part.
In other words -- $50,000 in transactions at 0.5% is $250 per month, which makes your 25% commission $62.50 per month -- for doing nothing.
If a business owner decides to pass 3% onto their clients, that means the processing company will make 1.5% on some transactions and 0.5% on others (as the true interchange rates vary by card type).