Well you would want to run the LFE. Because if you have your receiver setup right then you sould get low freq when you are playing something on a Stereo Track such as music; AND if you use the LFE movie's low frequency data which would be mixed out of the L&R will come out the sub where you want it to go. So set your receiver for a crossover of about 80Hz and tell it you ARE running a subwoofer and then you sould be in like sin (which like a lot BTW). LOL....
Currently im running the sub with the LFE output. Im just curious to know that if Im usinf the LFE im missing some low end information that the L/R rca contain.
If you have your Receiver setup correctly you should NOT be missing any information... Make sure that you have it setup so that the sub is on when you are listening to the two channel stereo format.