I have several tiles in my Rootsmagic software. My mother's line, my father's line, and my husband's. The reason I have them split off is that my relatives on my mother's side don't want to see my German ancestors since they aren't related to them. I did merge everything into one file when I realized my husband and I have mutual ancestors, so I could see how we were related -- 22nd cousins. As far as Ancestry is concerned, I do have everything in one file. However, Ancestry is for public viewing while my Rootsmagic files are for personal use.
As far as issues about Rootsmagic -- you can go to the Rootsmagic website and join forums there as well and get more info