With two roof faces, just run each through PVWatts separately and add the results together. It does not seem like there is any other way to specify multiple roof planes in a single entry.
You cannot file the SREC paperwork until PTO (you will need the signed interconnection agreement from PEPCO, which they should email to you when you get PTO,) though you can make sure you are prepared with the other documentation you will need. I'm not sure if you are planning on using SRECTrade or somebody else, but the SRECTrade application is pretty straightforward, and they handle all the interaction with the state.
The biggest application you will want to get in right away is the battery storage credit, since it sounds like you have PWs. While it appears there is plenty of money in the program, applications must be submitted by 1/15 and any issues fixed (I believe) by the end of January. Still plenty of time, but, unlike the solar grant, the battery credit seems to be based on the calendar year and has hard deadlines.