You can process your transactions offline if you want to, but...
somewhere on your monthly transactional statement, you should see somehere on there noted as the "qualification" of the transactions.
ie: on my statements from BofA...
on the bottom of the last page, there is a summary of X# of transactions qualified at x.xx% rate, Y# of transactions qualified at y.yy% rate and Z# of transactions qualified at z.zz% rate.
What that means is that for X # of transactions, you as the merchant paid X% to the bank for them to process the transactions for you.
The offline transactions (ie: hand keyed into a terminal) will normally qualify at a higher rate than say a swiped card.
An automated transaction will qualify at a higher rate than a swiped card too, but sometimes lower than the manually keyed transactions.
Automated transactions carry an ECI (ecommerce indicator) with them inside the banking systems, and therefore are auto-triggered as eCommerce related transactions.
For you as a merchant, if you are doing automated transactions, its MUCH better for you if you require the CVV number and force the BILL TO address to match the SHIP TO address. It still wont guard you from fraudulent transactions, BUT...it makes it a lot easier to defend against chargebacks.
Hope that helps shed some light on it.
I have been doing this in my day job for 15yrs now with some super high profile online storefronts, and it never amazes me what the banks do to manipulate the rates!
Later
Greg