Before you do ANYTHING, you have to calibrate the subwoofer levels using a test disc and SPL meter. Typically, you would want to adjust your actual subwoofer output level (the indicator level on your receiver is completely arbitrary because an additional adjustment on the back of the subwoofer unit needs to be accounted for) so that's its SPL reading is at least 4 db higher than the mains (this is due to decreased human hearing sensitivity in the lower frequencies).

Once you have the levels properly calibrated, then you need to go about making sure that your receiver is directing the LFE channel through the subwoofer output and not into the main speakers.

And with the terminology, the LFE simply refers to the low frequency effect channel on a 5.1 or 6.1 soundtrack (the ".1" track if you will). It's NOT synonymous with the subwoofer output. Any other bass that gets directed into the subwoofer output using your receiver's bass management settings is not a part of the LFE track.