Yesterday, I was speaking with a smaller contractor, a 12 person firm with no direct contracts with the government. All their work is as a subcontractor. One of their primes mandated that they get a DCAA compliant system in place. This will necessitate moving off of QuickBooks.
It's a myth that subcontractors don't need to have a compliant cost accounting system. The reforms in late 2008 made prime contractors responsible for ensuring the adequacy of their subcontractor's accounting systems and procedures. Prime contractors are besieged daily by smaller companies wanting to subcontract for them. If your company isn't compliant, the prime can find another sub that is, and they will. The best way to avoid that is to put a compliant system in place before your prime forces the issue. If you are proactive and take the steps to get compliant, and you market that fact to your primes, you will be in a position to pick up work when other subcontractors fail to maintain an adequate (by DCAA standards) accounting system.