Before everyone freaks out; please hear me out.
I understand that there are tons of posts on how to set gains, but that not exactly what I'm asking. I need help on where to begin to adjust the gains along with a parametric eq on my particular system. I hope someone can help me bacause I am about to pull my hair out because I just can't get my system to sound right. Before, I was using a factory head and the tonal quality sounded way better than what I have going on now. PLEASE HELP!!!!
Here is what I am working with:
Head Unit: JVC KD-R300
Speakers: Infinity 6002si
Type: 6-1/2" Shallow-mount
Speaker Impedance: 4 Ohms
Power Handling: 50W RMS
Frequency Response: 58Hz – 21kHz
Subwoofer: MTX Thunder 4000
Type: 10"
Speaker Impedance: 4 Ohms
Power Handling: 200W RMS
Frequency Response: 39Hz – 150Hz
Amps: Alpine MRP-F300, Alpine MRP-M500
The head unit has a parametric eq on it with the following ajustment options:

I had to upload an image because I wanted to make sure everything was understandable. Anyway Here are my questions:
What would be the best crossover setting? What do I want to have the eq set at when I am adjusting my gains? Can I use test tones, and if so which ones? I do hope someone out there can help me. Thanks all.
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2005 Honda Accord DX
Go to the Car Audio Hot Topics forum. There is a long thread on gain setting.
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Start simply, with the basics. Setting gain has nothing to do with crossover settings or parametric equalizers. The goal is simply to match the deck's highest clean output to the amplifier input so that they work in sync to provide full power without going into clipping. Set the amp gain, then work on crossing over the sets of speakers. EQ comes wayyy last.
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Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.