end up doing something VS. end up with doing something VS. end up in doing something
I agree with Edwin above. First, "End up" generally means "in the end, we did [x]," where x refers to something that is not a favorable condition or is contrary to what had been expected. "How was dinner at the new restaurant?" "I got sick. We ended up staying home."
As for the differences between the prepositions in, up and with, my understanding is that the meaning is largely the same. End up (verb)ing : End up eating out. End up with (noun) : End up with a hangover. End up in (place or condition) : End up in jail! (or) End up in a terrible situation!