Outlaw recommends that you set all speaker distances the same (on the DVD player)in order to get the sub phase in line with the mains.

If you set the distances differently, then the low pass information will arrive at the ICBM at different times, which will make it more difficult to set the phase. I think the impact is very minor unless you have big distance differences between speakers.

There is a thread on the Outlaw site that explains this much better than I just did.