I have not had good luck with making changes to both FTM and Ancestry.com and expecting them to be sync'd properly. My main tree is on Ancestry so I have learned to identify changes needed in FTM, then make the changes one by one in my Ancestry tree.
I've had so many problems just with the sync working with changes to only one tree, that to try to let FTM write to my Ancestry tree seems to be asking for trouble.
Yes, it is tedious to do it that way and I hope eventually the software will handle changes in both places. Right now, it's just too quirky for me to depend on it to do it right.