Sync data in only one direction at a time. If you modify the online tree, sync to FTM before changing ANYTHING in the FTM tree. If you modify the FTM tree at all, sync back to Ancestry before making ANY changes in the Ancestry tree.
Personally I do almost all tree changes in Ancestry, then sync to FTM. I then resolve places in FTM and sync those changes back to Ancestry. It doesn't matter which end you do your work on, as long as you have a consistent system.