"How do the Commercial Banks ever get repaid if the US gov't is continually running deficits?"
I assume that you mean "how does the Fed fund the repayment of reserve deposits to the Commercial Banks when QE is unwound, if the US Treasury is continually raising money to fund a growing US budget deficit"?
That might be a problem if the Fed was using commercial bank reserves to fund the US budget deficit.
But they aren't.
The Fed has used the commercial bank reserves to buy bonds from the commercial banks. Have a look at the Fed's balance sheet. http://www.federalreserve.gov/releases/h41/
I would imagine that at some point in the future, one of two things will happen:
1. The Fed will sell the bonds, which will remove funds from the US banking system and cause the commercial reserved deposits to run down; or
2. The bonds will mature, and the bond issuers - principally the MBS issuers and the US Treasury - will repay the Fed, removing funds from the banking system and causing the commercial bank reserve deposits to run down.
I think that you are confusing the management of the US budget deficit, which sits on the balance sheet of the US Treasury, with the management of QE, which sits on the balance sheet of the Fed. While there are transactions between the two, they are not managed on a consolidated basis.
