If I understand what you want, the Sync feature of FTM2012 will (theoretically) accomplish what you want to do. Keep a database on your ocmputer and also at ancestry.com, which always have the same info. From time to time, you can make a new gedcom on your computer from FTM2012 for WeRelate, etc.
That is, theoretically.
If you have been following this board for awhile, there are problems with Sync. This may effect a small piece of your file and only a small percentage of FTM users, but that doesn't count for much when it is YOUR file that gets screwed up.
I, for one, have no confidence in Sync and don't see using it in the (near) future.
If you decide not to sync, you will have to make all data entry in either ancestry.com or FTM2012 and then download or upload, as the case may be, from one to the other - the way we've been doing it for years - before Sync.