My impression (perhaps wrong) is that an LFE input does not include any sort of frequency filter (so it doesn't use a crossover), while the line-level inputs do use that filter. So, if your receiver is handling the crossover frequency like a lot of receivers do, then using the LFE input would work just great. If you use the line-level inputs and set the crossover on the sub to the max setting (which would normally be quite a bit higher than the crossover used in your receiver), you effectively do the same thing.