We used to use Quicken for Business, but never integrated. We just used monthly summary etc. We've also used MYOB, QuickBooks and PeachTree, but for what we needed Quicken for Business took care of things.
I use WHMCS for tracking income from customers in a general sense.. does revenue prediction etc too. I use Quickbooks to track expenses related to the business and running it. Modulesgarden makes a plugin for Quickbooks and WHMCS. I've never used it, but it sounds useful You can find out more about it here.