If you have any 18 hole roster, only 18 holes courses can be accessed when entering scores or setting home course, etc. 

EXCEPT if you are combining two - 9s to form an 18 hole score.  To do this..

1. Highlight the golfer and press F9....you will notice the nine hole courses are available on this form.


2. Highlight the golfer click the VIEW SCORES button.  On the Scores form click the COMBINE TWO NINES button.

If you want to track only nine hole handicaps, create a NINE hole roster.  Then ONLY nine hole courses and scores can be entered.  HS will calculate a nine hole handicap.