Multimeter readings

The reason your voltage output is lower at 100Hz, then, is because the crossover is cutting the output at that frequency.  That's what it is designed to do.  The reason you are reading 44V at 50Hz is you input gain is set too high.  You need to set the gain properly, IMO. 

Alright this is what I did earlier today:

Set sub gain with a 50hz track to 28.28v....when I switch the test cd to a 100hz track with the same gain setting at 50hz the voltage drops to 5v...it should stay close to 28v at 100hz right? I have the LPF set to 120hz so none of the frequencies should be cut off.

As with my coaxials....I popped in a test cd of 1khz, set gains to 14.14v...switched it over to a 2khz track...the reading remained at 14v. So everything seems fine with the coaxials but it's just the subwoofer that's giving me big differences in readings.

As for the RCA's I did what stevedart told me and these are my readings:

With my volume on the HU at 3/4 max and gains all the way down, I get 3.9v. If I turn the volume to max, it shows 9v (is that right?). These readings were stable regardless of frequency.  

For the subwoofer setting on the HU I turned it from Mono back to Stereo...it sounded a little better but maybe I'm just imagining that. I switched the Media Expander feature on my HU on and it made everything sound 5 times better...is it okay to use this feature?

I also turned down the subwoofer setting from +15 to 0....I think you were right about it being an attenuated...the readings on the multimeter went from 3.9 @ +15 to 0.5v @ 0.

Is there a reason why I am supposed to set gains using a 50hz test track? I have my subsonic at 25hz....is this even at the right place?

Thanks for being so patient. Hopefully you guys haven't gotten fed up with my questions yet.