Hi Leanne,
We are going through that exercise right now and, it will relieve us of having to take phone calls and information and then processing through our terminals. We set it up via our merchant bank who also looks after our credit card terminals, and was straight forward. We just had to sign a new agreement for the website and was separate from our existing credit card agreement. As we have not gone live yet I cannot attest to its popularity, but a lot of clients had requested this flexibility leading up to this project. From our testing reconciling should not be difficult if you currently take credit card transactions, it works basically the same.
Thanks