We've never worked with GiftWorks before, but we've heard really good things about it. After some research, it looks like GiftWorks Live integrates with GiftWorks, which then integrates with QuickBooks. Unfortunately, I couldn't find anything that showed a direct integration between GiftWorks Live and QuickBooks.

I'd have to know more about how the integration works before advising you about how to do it right.  However, I can tell you that using classes in QuickBooks is critical.  Your class setup should look something like this:

Unrestricted Funds
   General & Administrative
   Fundraising
   Programs
      Program 1
      Program 2

Temporarily Restricted Funds
   Grants
      Grant 1
      Grant 2
   Capital Campaign

Permanently Restricted Funds
   Endowments
     Endowment 1
     Endowment 2