I have FTM and each time I add to my ancestry.com tree, I then at some point need to open FTM and tell it to sync up. If you open FTM first, it checks to see if the tree needs to be sync'd up with ancestry.com. Also if you have added a completely new tree to ancestry.com it can be linked to FTM easily.
Not sure if I answered everything you wanted, but all photos, documents, everything in one tree on ancestry.com will sync to the FTM tree.
Changes can be made to either the FTM tree or ancestry.com and then sync them together and the changes will appear in the other one.