Don't know about the Ancestry tree 'cause I don't use it much, but The Master Genealogist (and perhaps other desktop software) allows you to create your own relationships. I use several of my own inventions frequently, such as PossiblySamePerson to link records for two people with same name, but not sure they're the same person. Also I use Witness, Minister (at marriage), SoldLandTo, BoughtLandFrom, Executor, Neighbor, Census (for same household in census) or anything else I can think of that might be useful. I agree that you have to keep track of as many associations as possible, especially when working with difficult problems.
Maybe you need something more robust than Ancestry's trees to keep track of these families?