What I ended up doing was to use the joomla template i had already made and use the divs and css to form the header and footer files for whmcs. I had very successful results, although my main menu has to modified manually. Thats no great problem though. It took me about 3 or 4 hours to figure out the templating system and modify my joomla template to suit.
You can see my integration at http://www.denovodigital.com . Its not finished yet, so it still looks a bit wishy washy, but I'm pleased with how its progressing. I would seriously reccommend adding the same doctype you have on your joomla template to the whmcs one. It makes css styling a hell of a lot easier.