There are many other threads on this board discussing issues with migrating data from FTM to FTMM.
The best method (fewer things that can go wrong) is to use the Ancestry member tree program. Upload/sync the FTM tree to Ancestry member tree program, then download the Ancestry to FTMM.
There's a detailed explanation on this board of how to perform this maneuver. Take a bit of time and read some of the threads.