Jonno said:

Your subwoofer won't be neglected, since your receiver will filter off the lower frequencies of the mix for it (DS mixes don't tend to be all that bass-heavy, but they can surprise you).

Technically isn't separation of the bass frequencies between mains and subs a function of the crossover setting in the receiver? For a properly balanced system the subs would take over just above the lowest reproducible frequency of the mains which would then be free to output only the range of sounds they are capable of.

For matrix mixes this is fairly straight forward since there is no discrete LFE data. I assume for discrete mixes, depending on where the crossover is set, part of the LFE data might actually be going to the mains, but I've never really thought about this (or tested it) before.