We have done this with the help of Ronnie from http://www.whmcsconnect.com
I was a bit unsure at first, but his help has been great, and they work well together.
Odd, I still seemed to have to pay WHMCS, even tho I had bought iWHMCS before, it still would not let me use it apart from the main screen, so had to part with $29.95 - Kinda sucks Matt....