"we found the sub-woofer needed at least a 3ft distance from the docking station to get a decent separation of sounds."
The whole point about sub-woofers is that the ear cannot tell where they are, because they only emit low frequency sound which lacks a directional component. That is why you only need one of them in a stereo or multi-channel system, and why it shouldn't matter where they are placed relative to the other speakers (although it does matter where they are placed in the room, due to "room modes"). To talk about "separation of sounds" is nonsense when the separation you want is between left and right channels, not high and low frequencies, the subwoofer being a mono device reproducing low frequency components from both channels. In fact, you want the opposite - the high and low frequencies should blend together to sound natural.