You have them set to all pass which means the amps crossover is bypassed
Since your running components with passive crossovers then then you don't need the to mess with the amps crossover
You can set your gains (input level) with a multimeter and test tones
Here is a how to on it
You can download the test tones from the JL audio website
As for the cross over on the sub amp I would start at about 80 hz and then play with it until it sounds right
Just make small adjustments and then listen for a day and then re adjust if needed
It takes a long time to get them just right
Hell I used to always play with mine, now I have DSP so there are way more settings to play with
It kind of comes with the territory
You can set the gains on your sub amp the same way and the punch EQ is a user specific kind of thing
You just have to play with it until you like the sound