Syncing works both ways. However, syncing will not happen from your old Ancestry tree; it will upload a new tree from FTM 2012. You can either keep the old ancestry tree and thus have two trees on ancestry, or delete the old ancestry tree.
Warning: if you ask ancestry they will say download your ancestry tree to a new ftm tree and merge. For most people using ftm as your primary that is NOT a good idea. But a beginning sync will make a duplicate either online or on your computer, no way to avoid that.
I do sync, and I do like it; but I have diligently been working on my FTM tree to make it independent of ancestry in case I lose the sync for any reason. It has taken about 18 months but I finally finished THAT project.