Yes and no. When you join Top Eleven you are given a Level 1 team. If you join in the middle of the season, there is a chance that your team is not in the Cup anymore (and there is a chance that it is still there).
As I did some times a "take over" (a new club from the beginning), I noticed that usually (if not all the times), when you get a new team after only few days of the season, it's always out of the Cup.
I think the game could choose for the new manager a team which is in the next round of the cup as most of the competitors are bot teams.