I have four subs of various lineages and distances from my listening position and I believe phase, balance(vol.) positioning, for me, are MUCH more important factors in good sound than a couple of feet here or there in measuring distances. I wouldn't worry about it. You could have the distance set perfectly but if the above items are not set to their optimum, it isn't going to make any difference.
The other issue you asked about LFE outs on AVR's has been a bone of contention of mine for some time now. When you look at the increased sophistication, inputs and outputs for everything else yet only ONE sub out? Ridiculous, and when you ask this question of the retailer/distributor they just shrug their shoulders. Pre-pros of the recent past have usually been the ones with multiple sub outs but even there, they are cutting back. It seems the only way you can get around this is spending the extra dough to buy a unit like the Velodyne SMS-1(I have one) or this forthcoming Audessey sub unit from SVS or some other multiple sub crossover unit which tend to be found more in musical instrument applications, otherwise your basically left with daisy chaining subs together with Y-plugs.
