Well, first things first I guess...Should I be using the Anthem crossover or the REL crossover? Does the Anthem crossover apply to both high and low level REL connections?
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I suggest you download the Manual from Anthem Website.
You have the ability to control the individual level sent to each speaker including the sub. It sounds like you need to adjust the levels first and then play with the crossover.
The notch filter only works on the sub....so it is probably your REL Storm which is getting too high of a signal (wrongly connected). Connect the second sub to the sub 2 XLR jack with subwoofer set to "2 sub" or "2 super" 9see page 45 of the manual). Recall that with speakers set to "FULL then "2 Super" takes all the LF channel information and combines it with the LFE channel and sends it all to the sub. If you are watching a movie the "2 Sub" setting will be better (Cinema configuration) for stereo you may want to use "2 Super"
Anthem AVM 20 Owners Manual