I have some divisions that are scheduled to play less rounds than other divisions, how do I indicate that? I don't think I want to use a 999 code as it would then mark those players as a DNF.

Right, you only want to use a 999 or 888 code for a player that didn't complete (or start) a round that they were scheduled to play.  In this case, simply leave the scores blank for the rounds those divisions did not play.