To tell the truth, it doesn't really matter.
The fact with a sub is with low tones, the ear doesn't notice where its coming from like it does with high tones.
Wherever you put it, the sound will seem like its coming from the speakers themselves.
Though I'd put it on the same side of the room as the speakers, though can be on the floor or on a desk somewhere in the room. If its a surround setup like it is, the best place would be the middle of the floor, though this isn't advisable