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In my fiance's car, she went from the stock head-unit using speaker level outputs to an aftermarket top of the line panasonic head-unit with 5v preamp outputs and the bass SQ is much better, but it seems quieter.

I was thinking that it may be the head-units 120hz LFE Crossover, but the MTX amp has a 200hz LFE anyways....

To the get the same volume that we used to get, I have to set the gain to full, and the bass-boost at 3/4's which doesn't sound right because, before they were about half and half.

 
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If anything it should be louder.

I would scroll through the features of her HU and see if there is a preamp level adjustment for the sub output. I know kenwood has a level adjustment feature in their headunits which will cause the volume of the subs to be quieter or louder.

Preamp outputs will give the amplifier a stronger signal than speaker level inputs which will allow the amp to reach its full potential (like it's maximum output) especially with 5V preamp outs.