Alright hopefully some people are still checking this thread because I did a couple vids today showing the "breathing" effect to show exactly what I'm talking about so everyone can understand what I'm talking about now haha.
First video is the amp running directly off my Galaxy S III playing a -5db 40hz tone which I retuned the amp with the SMD specifically for running this track off the S III.
https://www.dropbox.com/s/rz3yo0hmolk71pt/VID_00000004.mp4
Second video is everything hooked back up the way it was and retuned back to -5db with the SMD for the Head Unit. You can see the subs do the "re-align" in this video at about the 1:05 mark.
https://www.dropbox.com/s/ew3jyb9gcxux22v/VID_00000005.mp4
Check out the vids and let me know what you guys think and if I should be worried about damaging anything.