I couldn't find scorecards for the 3 courses, but presumably you have them (or can get them). If I were a member of GolfLink (through the golf channel), I could only view the one for the Whispering Pines - there wasn't one available for Meadowview or Hillside.
Anyway, check those cards closely, as they often include a rating and slope for combined courses. If they do, then you'll have to create three courses, one for each possible combination. I wouldn't go as far as entering another course with the back nine first, then the front nine - just enter your scores that way if/when you play them in reverse order.
If they don't have this information talk to the pro shop and see if they have any "unpublished" information on the ratings of the combined courses. If they don't, then you'll have to "make up" your own ratings, probably based on how you (and your friends?) play the course.
Otherwise, you could just enter the nine as you play them and let OOB combine the 9-hole rounds into one 18-hole rounds for you. Really, it's not that much different than playing two 18-hole rounds in one day.