My home course has two vastly different 9s. While similar in length, the back nine is more difficult due to significant terrain changes, some forced carries, natural grasses areas which are not marked as hazards or drop areas, and over the course of a season, can become quite long and thick. This leads to lost ball penalties. The back also has a far greater exposure to the wind. People I have played with will play the front nine from the "White", then play the back from the "Senior" tee box. I think most of them enter their scores as a total for the round, usually from the longer tees. If you just enter the scores as two 9 hole rounds handicapping is no problem.
Mixing tee boxes, did you adjust slope and rating for hcp. purposes? Where could one fine the info necessary to do that?