Do you always prefer to run your mains full range and integrate the sub at the natural roll off? I was thinking I would use the 80hz crossover on the sub amp to better integrate and reduce the load of the mains. The directionality of the higher crossover is why I was also thinking they should be forward facing and directly under each main speaker.
Even at 80Hz the signal is still omnidirectional so driver direction doesn't matter. As an aside, 80Hz is the THX standard crossover point.
The numbers on the crossover dial of the sub amp don't actually correlate to a specific frequency so you can't just set the dial to 80Hz and actually have an 80Hz crossover point to subs. Having some way of measuring the signal is a lot easier than doing it by ear. I use REW.
If you are going to let your speakers roll off naturally, you want to crossover where the speakers are -6dB. With the X-LS Encores that's around 51Hz but could differ due to room gain. If you want to roll them off higher and you have a separate preamp and power amp, you can use an inline filter between the pre and power amp to change the rolloff and thereby the -6 point. If you are using a receiver with bass management, like an AVR, you can use it's bass management to set the crossover point. In this case you would connect to the LFE input on the sub amp. This by-passes the sub's crossover controls.