The web site is a little weird, but you should be able to book in both directions. I just tried and was able to see seats from KL->Singapore: http://www.transtar.com.sg/olcoachquery.php

You could also try doing it over the phone. Calls to Singapore and Malaysia are normally free or cheap (no more than $0.03/min) with discount calling services.

If Transtar is full, there are a zillion more companies - less fancy but still reasonably nice buses. My friend uses First Coach. I've used Grasslands (aka Extra Nice) several times. It's cheap but there are three seats across (one on the left side and two on the right side of the aisle) so it's not quite as spacious. Aeroline is well-known but I don't find it to be good value.