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Personally, I would stick with a standard 3d cartesian coordinate system - that means using infinitely small points, referenced with vectors (a 'point' in space being made up of an x,y & z coordinate)
There are plenty of 3d vector classes available that already do all (er, alof of, anyway) the math for you. (Let me know if you cant find one, and i'll send you my own (in c++))
If you only allow objects/actors to occupy the center of a space (whatever shape that space takes), then you'll have actors in the same room all occupying the same space, and you'll lose any benefit you would otherwise gain from using a 3d coordinate system in the first place.
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