Marathon 2: Durandal (http://www.speedrun.com/Marathon_2_Durandal) is a PC/Mac game that has an Xbox Live Arcade port. Currently this is noted as having Mac and Xbox 360 checked for possible platforms. However, the XBLA port differs significantly from the original game (the engine is completely rewritten and runs at 60fps instead of 30), so I want runs of it to be in a different category. What's the "right" way to do this?

I ended up setting another variable for PC/Mac vs XBLA and setting it as a subcategory.

Subcategory is the best way to do it generally. Sometimes these get split out into separate games as well if the games are different enough.