Unfortunately, you're in a pickle. You need to collapse these trees into one so you can save yourself time and take advantage of FTM 2012 (FTM 12 refers to an older version of the software before years were used) and its TreeSync capability.
I say unfortunately, because there is no good way to do this. FTM does offer a way for you to import one tree into another, and it's supposed to identify duplicates in the process, but in my experience it doesn't work. That shouldn't stop you from trying though. Just be sure to make backups of anything you're messing with.
To make things easier, I'd recommend downloading your tree at Ancestry.com, but not as a linked tree. You'll then have two separate FTM files, one for each tree. You can then try the file merge stuff, but be careful to check to see what happened when duplicate people were merged. (I find duplicates remain and the facts get all messed up even when people are merged. Also, if you're not careful, it will merge people who are not duplicates.)
After you give up on trying to use FTM's automation, I recommend that you come up with a game plan to say manually merge 50 or 100 people a day. It'll be worth it when it's all done, even if it takes several months to complete.
Hope that helps.