I should point out that I am using WHMCS and the 2 plugins that go with it as well. I am however trying to use Pro Sites to keep my Free users separate from the paying (WHMCS) users. So Free users can sign up with the wp-signup.php file page nice and easy. Only problem is since we installed WHMCS the upgrade part of Pro Sites does not work. When you click the upgrade button you just get one of those 'No Results Found' pages.
I tried bypassing it (which I want to do anyway) with.. wp-signup.php?webmaster-pro=1 when they sign up but that doesn't work either. It creates the website and adds the user etc. but it will not upgrade the user to any Pro Site level.