Who is telling you to do these things?
If the woofers/amp on your speakers have a line in then it seems there's a choice of using them with the subwoofer pre-out from your avr, or not as you are now. Using the speaker via the speaker level input would be the alternate and is probably a decent plan but I'd still set them to small unless your subs/shakers aren't up to the task, then set them to large.
The LPF of LFE of 120 setting in the avr is just affecting content that has the .1 content (5.1 original content, 7.1, etc); it's not about redirected bass like when you set the speakers to small. I'd turn the low pass filter on the sub to max as the avr is doing the bass management; duplicating the low pass filter in both the avr and sub isn't generally recommended.
Spend some time with them in the various different possible settings and use the one that puts the biggest smile on your face.