In my opinion, making your FTM file your "main" file is better, using tree ancestry tree primarily for publication and to possibly enter data when in a remote location - like a library or genealogy trip.
I have seen too many problems with syncing. I won't be syncing for quite awhile until ever - depending on whether these things get fixed. I don't feel I need it.
As to your second question, that is why sync was introduced. Unfortunately each separate upload is a new tree, with a new url and creates a second file, which should be deleted. This requires notifying people that your file has moved. Or, they can find you by re-searching their name and looking for your tree name.