I'm assuming your FTM tree and Ancestry tree are unlinked, but your FTM tree is online, and you have been using Web Search and Merge to load "documents". I'm also assuming your tree is not huge and your goal is to bring your FTM tree into "compliance" with your online tree; and by documents, you don't just mean media, but also people, and records with sources and citations. If so, the basic idea is: don't try to figure out what differences exist between the two trees, but eliminate them, or at least minimize them.
The method is to create a new FTM tree by downloading your online tree, and then merge that tree with your original FTM tree. It is essentially a one-way sync, i.e. the method only transfers data from your online tree into your FTM tree. Before doing all this, backup your original FTM tree by copying the several files to a safe place.
For me, the option to create a new FTM tree by downloading an Ancestry tree is functionally gone in both FTM 2012 and FTM 2014. The option reverts to creating a GEDCOM file which you then download. Of course this file has no media. If you can create a new FTM tree by truly downloading your online tree, do it, and then merge the two FTM trees.
However, if you end up with a new FTM tree created by a GEDCOM, open both your original and new FTM trees (preferably side-by-side half screen) and make note of the number of people and sources in each tree to get a rough idea how far apart the two trees are. Then close-out the new tree window and merge the two trees in whatever direction you prefer. All the people, sources and citations from your online tree are now in the merged FTM tree. It would be a good idea to also backup the new FTM tree files before starting this process.
Media from your online tree that is not in your merged FTM tree can be found several ways. For FTM citations with media, look for missing media icons in the various citation lists. The media can then be copied from your online tree to your computer, and ultimately into your merged FTM tree. Other missing media can be found by going to the FTM Media workspace and selecting list by person, and then compare the FTM media gallery for a given person, with his or her online tree media gallery. You can use side-by-side half screen for each tree, and if need be, use your browser to scale down the online gallery. Census media and other citation media will show-up in your online gallery, but not in the merged FTM tree. So don't try to copy this media into a person's FTM media gallery.
To avoid all these headaches, it may be worth upgrading to FTM 2017 and using the sync function, particularly if you have a large tree.
The method is to create a new FTM tree by downloading your online tree, and then merge that tree with your original FTM tree. It is essentially a one-way sync, i.e. the method only transfers data from your online tree into your FTM tree. Before doing all this, backup your original FTM tree by copying the several files to a safe place.
For me, the option to create a new FTM tree by downloading an Ancestry tree is functionally gone in both FTM 2012 and FTM 2014. The option reverts to creating a GEDCOM file which you then download. Of course this file has no media. If you can create a new FTM tree by truly downloading your online tree, do it, and then merge the two FTM trees.
However, if you end up with a new FTM tree created by a GEDCOM, open both your original and new FTM trees (preferably side-by-side half screen) and make note of the number of people and sources in each tree to get a rough idea how far apart the two trees are. Then close-out the new tree window and merge the two trees in whatever direction you prefer. All the people, sources and citations from your online tree are now in the merged FTM tree. It would be a good idea to also backup the new FTM tree files before starting this process.
Media from your online tree that is not in your merged FTM tree can be found several ways. For FTM citations with media, look for missing media icons in the various citation lists. The media can then be copied from your online tree to your computer, and ultimately into your merged FTM tree. Other missing media can be found by going to the FTM Media workspace and selecting list by person, and then compare the FTM media gallery for a given person, with his or her online tree media gallery. You can use side-by-side half screen for each tree, and if need be, use your browser to scale down the online gallery. Census media and other citation media will show-up in your online gallery, but not in the merged FTM tree. So don't try to copy this media into a person's FTM media gallery.
To avoid all these headaches, it may be worth upgrading to FTM 2017 and using the sync function, particularly if you have a large tree.