I've honestly never hooked a sub up using the speaker terminals so cannot say from experience there is a degradation. I know it doesn't "feel" right in my gut so I opt for an RCA cable from a second set of preamp outputs to the LFE input. Either the left or right is all I use for very low bass.
When it comes to audio only I usually just set the crossover very low and the level at zero and dial it up slowly and set it by ear. Hypocritically, in the HT, I'd make sweeps and plot graphs to see what is going on. I have found that with full range speakers not much, if any, sub work is needed. I think it can be trickier with bookshelf speakers as you are asking the sub to perhaps play higher (to fill in a gap perhaps) and subs may or may not be "musical" in those 60 hz+ regions.
If I had to connect the sub using speaker cables I'd try a second parallel run from the amp or jumper over from the main speaker versus the other way around. For me, a sub in 2 channel is supplementary and will be cradling the bottom end and not really doing much work.
Do you use full range floorstanders now?
