There is a substantial amount of information that would be lost if the sub was not hooked up to the HT. The entire LFE (Low Frequency Effects) channel would be lost (the .1 in 5.1)
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If your use would be 75% music and 25 percent HT then I would suggest using a REL subwoofer as you mentioned. I have used the LFE connection for HT and the direct speaker output connection for music. My suggestion is to find the space to place a Storm III or a Strata III. You will not regret the purchase. I owned two different Sunfire models and found that they were great for home theatre but did not integrate well with my speakers in two channel stereo. The B&W Subwoofer did not integrate as well with my speakers as did the REL, my main speakers are B&W N803's.
Swampwalker> This has been my thinking as well, however I have also been advised to connect to CJ and then set processor to large front speakers and the rest small. Set sub as no or equivilent and then all bass will go to fronts and thus to sub. Does this seem right? It does to me but then again your point about the 5:1 makes sense also. Is this a workable compromise?
Artemus, recently I've been looking at subs. I took a look at the Martin logan page. The new Descent sub. I opened the manual on descent and it showed the descent being hooked up as 2channel, ht and both at the same time. From what I read it looks like the descent will take both connections at the same time, giving you both ht and 2 ch.. The sub has 3-10 in subs and a 400 watt amp. Abit pricey @ $2,400. I never auditioned it, but if you do a search here I think you'll find someone who ownes one. Good luck, pete