LFE is mono, so even if you use L&R it will be summed back to mono by the sub.
If it is a powered sub, which it sounds like it is, you cannot power it with an external amp. Hooking it up via speaker level, the sub will simply strip the signal out and does not use the power from your receiver/amp. If the receiver doesn't have a preout for the sub, use the L&R and adjust the x-over via the sub's x-over control.