My opinion is that for most of us the LFE out is the cleanest and most efficient connection method. Itâ€™s clearly the easiest implimentation. It makes calibration a snap. Not all people feel this way. Some people love using the variable x-over on the sub as opposed to the fixed one on many receivers. After experimenting with the speaker level connection and measuring ad naseum, I ended up back at the LFE out connection as (with my equipment and in my room) it clearly yielded the flattest bass response. I also found the audible difference between say and 80 and 100hz x-over to be overblown. Here's a link to my experiment and results if interested.
Using the speaker level input on your sub and setting sub to "No" would not work out well, since these connections are mostly used for bass augmentation mode, where it picks up where your man speaker starts to drop off. And with the dirverted LFE to your main speakers, that means the mains still takes the full LFE signal. That is unless your speaker level input has some sort of passive high pass filter. But I wouldn't use that either since it is so inaccurate.
If you are connected via the speaker level outputs rather than the line level, you don't have a choice. The sub needs to be be set to NO. The whole Idea behind the speaker level connection is to tell your receiver there is no sub and send everything (includung the LFE) to the mains. You then slip the sub into the path and use it's Low-Pass Filter (x-over) to filter the signal.
Setting the sub to YES (if your using the speaker level connects) would send a signal via the line level output which will go nowhere because it's not connected. At the very least, the LFE will get lost and maybe more depending on how your receiver's handles the bass mgt and whether you set your mains to small or large.
I don't use the LFE out, instead I have set the mains to large and no sub. In using the sub with mains approach, it allows me to set crossover freq down to around 50hz. I could also set different high pass and low pass freq in order to blend it better. In my base, 40hz high pass and 50hz low pass. Plus my center is also set to large and it crosses onto its own sub @ 155hz. I am still experimenting with high pass @ 131hz and low pass @ 155hz..
To do the above, you can't just use the crossover knob on the subs, but you will have to get a active crossover that has seperate high and low pass freq adjustments.
I looked at this question and wondered. Best results using what equipment and situation? I think my LFE out works correctly for home theater DVD viewing. But when I listen to stereo music I hit the Niles switcher and bring better equipment into play with my tweaked out tube amp and Phillips Labs pre. Then at that point I enable the crossover on my SVS sub feeding the correct signal to my high efficiency Aria 5Rs. My AVR has a crossover point that is not low enough so using the crossover in the SVS works properly for me in the stereo music mode.
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