I'm on RootsMagic4, but the technique should be the same.
One of your FTM trees should be in GEDCOM format.
First create a new tree by importing from the FTM file.
Then import the GEDCOM file (File, Import) and select "Combine into the database".
Finally, run a Merge (Tools, Merge).
I would run a Duplicate Search Merge first, followed by an Automatic Merge, SmartMerge option.