Sorry it took so long to get back to you... it's been hectic around here.
PayFlow Pro is what we use at work with a client. Seems to work for them. I developed my own PHP class to be used inside cakePHP to do both the sandbox testing and the live transactions. I can't give you that code because of an NDA; however, I can say that the PayFlow Pro documentation is extremely helpful and very detailed. Eventually I may write a full PayPal Class to do this, but not right now.
I haven't used any other online merchants. They're all basically the same though. Ninety percent of banks will work with online merchants. If they didn't, you wouldn't be able to purchase items online 😉 The only part your bank will notice is (1) deposits to verify you are the account holder and (2) transfers you make from your online merchant account to your bank account. If you wanted to be a litle more quarky you could get a ING account, use that for all your online stuff. Then transfer from your ING account to your bank. It's nothing more than wire transfers as Kudose said.