I seem to have a lot more voltage drop to rear fuse to amp when the seats are up, rather than down. This is a trunk car. Is lack of air flow making the sub work harder?  I have the rear 6x9 vacant..

 

Seat up/seat down could be changing the final alignment of the sub + enclosure + vehicle, which is changing the impedance curve of the subwoofer. If the change is significant enough and the impedance over certain bandwidths has decreased compared to seat down, the amp could need to output more power over certain frequency bandwidths and as a result would draw more current. If your electrical wasn't able to supply the additional current, the voltage would drop.

How are you measuring the drop and how much of a difference is it? I assume the issue with voltage drop occurs over the entire electrical system and not JUST at the fuse, which could indicate a different problem.

My volt meter is reading from the fuse prior to entering the amp.  Its almost a volt difference while playing a tone or same song/note @ same volumes. 

 

Waiting for Xmas until I get my mechman 240 =\, I know my batteries are not getting charged the way they like.  Thanks for explaining the physics, however.