guidence for setting gains

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.