Banks will typically charge 2-4 times more for their proprietary software or for the same software you can find elsewhere for far less. Better card processing software will maintain a database of entries to provide a transaction record and to simplify processing repeat donors. Check in advance that your bank is on at least one of the credit card networks the software you purchase can work with, but it almost certainly will be unless it is very bad software or your bank doesn't use the common credit card networks. Monthly account fee. Annual account fee.
Some banks use a monthly fee instead.
Ask if you'll be billed in advance, after six months, or after twelve. This is a fee based on the amount of the transaction. All banks charge this fee. Per-transaction flat fee. If the bank charges this fee, its per-transaction rate will usually be significantly lower than those that don't.