The combined entity will operate out of T2 for the foreseeable future.
Eventually, AA is slated to move into T1 after it is renovated. The renovation has been approved but hasn't begun yet. In July 2013, the airport commission approved the T1 redevelopment plan, which is scheduled (currently) for completion in 2023.
As this is San Francisco, it's reasonable to expect some delays beyond the target completion date. In fact, initial phases scheduled to begin this summer haven't quite started.