1.       I just got an Energy S 10.3 subwoofer. I want to use this with my Energy Connoisseur speaker system and Pioneer Elite receiver.

2.       I have – to my knowledge – have the correct receiver and speaker settings:

a.       Subwoofer is on and selected in the receiver (responds to test tones etc.). I have very high quality subwoofer cables.

b.      Have set the cross-over at 80 Hz and matched that in the subwoofer setting

c.       I have tried flipping the activate-deactivate cross-over

d.      Tried tweaking Bass-Peak level in the receiver and have set it to -25db

e.      The indicator LED shows that lower frequencies are being passed on to the woofer

What am I missing here?

1) I'm not sure why you have cables.  You only need one.  Quality is indistinguishable between different ones.

2) You should never use 2 crossovers.  Deactivate the subwoofer's.  If it can't be deactivated, then set it to the maximum allowed value so it doesn't interfere with the receiver's bass management.

3)  "Tweaking" is what, exactly?  Your goal should be a flat system response which you achieve with a setup disc and an SPL meter (or an auto-setup if the Pioneer is so-equipped).  A flat system, generally speaking, shouldn't "thump."  The subwoofer should blend with the rest of the system and never create a sound that you can identify as coming from the subwoofer.  If you end up with a sub that booms and thumps, then your setup is seriously out of whack.

4) Your receiver likely needs to be told to send sub-80 signals to the sub (setting the crossover doesn't necessarily do it).  It may only be forwarding the LFE track.  Set the sub to "Main/LFE."  Set all of your speakers to small - no speaker should ever be set to large.  See:

http://www.audioholics.com/techtips/setup/loudspeakers/bassmanagementbasics.php

    The above post is correct assuming that you want to use the sub LFE jack-which is the same as a single RCA.

Another alternative, which will provide superior bass response-is to attach the sub using the actual speaker leads.(for your front speakers) The Energy user manual outlines how to do this, attach the front L+R into the in jacks on the back of the sub, and then use the subs out jacks to your front speakers. Then set your receiver so that it thinks there is no subwoofer, low end frequencies are directed through the front speakers terminals and into your sub; voila, awesome bass! This is how a true audiophile sets up a sub.

aasenatrix:

Another alternative, which will provide superior bass response-is to attach the sub using the actual speaker leads

That is in no way "superior" to the receiver-managed method.  In fact, you lose the ability found in most receivers to time-align the signal accounting for distance, delay, and response of the subwoofer, so the sound will almost certainly be inferior.

aasenatrix:

Then set your receiver so that it thinks there is no subwoofer, low end frequencies are directed through the front speakers terminals and into your sub; voila, awesome bass!

The LFE channel is never redirected to the main speakers due to the volume differences in the signal encoding, so your method will completely lose it.  Again, not very awesome as any 5.1 audio track will become 5.0.

aasenatrix:

This is how a true audiophile sets up a sub.

"Audiophile's" don't own or use subs... period.  They're also typically gullible and foolish people who equate money and quality as having a linear relationship.  If you want to go broke, listen to an "audiophile."  If you want a quality system for a reasonable price, look elsewhere for assistance.