not a problem man there will be gain,bass boost, HPF, and LPF.
1. Do NOT turn the bass boost up leave that at 0
2. the hpf is what your going to be using. Its a guessing game from here on out unless you have an O-Scope. for your 6.5's i'd suggest turn the dial till its at about 65-75hz, this will start to cut out the frequencies below this point. For the 5.25's i'd personally guess about 100hz or a little higher.
3. Next is the gain do this for each set of speakers at a time tune one then unplug them and tune the other set. If you listen carefully you'll realize when you've reached your speakers limits and you'll hear distortion its when the music become unclear and has more of a harsh sound to it. also if you see your speakers moving to much either turn the gain down or turn up the hpf. since you are still noobish(no insult meant) i'd suggest turning both down slightly.
4. Once you've done this for both speaker hook both sets up and see how they sound and do any final adjustments that you feel are needed and when tuning the sets one at a time play a wide variety of songs because some songs have a stronger signal then others and will cause some songs to sound horrible and some to sound great.
Any other questions feel free to PM me