if you have FTM 2014 then you download your ancestry.com tree into the program. Run clean up tools, "Find duplicates"; "Resolve place names"; "convert names". Then run backup.
then do the same thing for your 2nd tree.
Pick the Main tree and merge the trees together. Run the clean up tools then sync it back up to ancestry.com. Make sure you delete your old tree but back it up before deleting it