Credit Card Processing Fees

I find this confusing. I have several sets of fees and unless I make an effort to see them all, they're never presented in one place.

I get a monthly statement from the bank which has two sets of fees on them. These are the ones associated with the type of credit card (qualified for discount or non-qualified as in the credit card vendor is proving miles on discounts back to the card-holder....which they are charging us the vendor for).
In addition, my ISO hits my bank account once per month with fees. Overall, these add up to about 3.5% of my revenue which is into 7 figures. Is this appropriate or over priced?

As I look at other approaches, I see at Paypal that the pricing for Payflow Pro is:
Set-up Price $249.00
Monthly Price $59.95
Included Monthly Transactions Up to 1,000
Additional Transactions $0.10 per transaction

But then, The prices listed are for the Payflow gateways only and do not include additional fees that your bank or card association may charge.

I'm guessing that this means that this is in addition to the credit card fees. I'll be looking into this is some real detail in the next month or so.