Headunit Amplifier Settings

I have a new Alpine headunit with built in crossover settings, and three Alpine aplifiers.  One for my highs, and two for my two Alpine subs.  I really don't like messing around with the settings for my crossovers on the headunit.  I would rather just put the deck on DEFEAT and use my amplifier settings.  What do you guys like to do?  Also, with my amplifier gain settings.  I know how to set my four channel.  I unhook my sub amps and turn the gain settings all the way down on my amp and then turn the headunit volume up 3/4 of the way.  Then I adjust my gains and crossover accordingly.  But with my two mono amps, when I go through to set them on my subs I notice that at the exact same settings on the amps the subs are not playing at the same level.  Is this normal/unusual that two of the exact same amps need to be adjusted at different settings to get the subs to be close to equal??????  Would this have anything to do with my splitting the one sub output off my deck, or the mono/stereo output setting?  All of my components are brand new so I know there shouldn't be anything wrong with them. 

OK first I would defeat the crossovers on the headunit use the ones on  the amps,  As far as the sub amps they may not be set 100% the same. How can you tell they are not performing equally, are you only running one at a time to see this. I woud set the gains accordingly running only 1 sub at a time. The mono stereo setting is this on the amp, if so are you running the amp bridged or mono. I bet if list model numbers someone familiar with the exact model will respond more detailed.

Yes, all three amps are Alpine, and the two sub amps are the same.  I have the four channel hooked into the front and rear RCAs on the headunit and the two sub amps are hooked into the sub output on the headunit.  I used Y splitters to break the HU output for the two RCA's which I ran to the amps.  My four channel is hooked up to the HU remote turnon and the sub amps are both on separate switches coming off of the ignition 12V.

My four channel has an output but my sub amps don't, so this won't work.

what model #s are the amps and subs

Two MRP M-350 mono block sub amps and one MRP F-240 four channel amp.  My subs are Alpine S-Type 4ohm DVCs.