I have a pretty crazy, but accurate tree. Both my parents' lines are in one tree, BUT, my Dad was adopted, so a good portion of it is moot. Further, I have included my ex-husband's tree as well, and administer his DNA test. So both tests are linked to the same tree.
I have a great deal more matches than the ex does, but there has never been any confusion on Ancestry's part between the two tests and the one tree.