Multple crossovers, HU, amp, speakers?

As I continue to tune my system that consists of:  Alpine IVA-D310, JL Audio 500/5 amp, JL Audio XR650i's and JL Audio 8W7 sub, I keep thinking that there are so many crossovers to deal with and am I doing something wrong?  I followed the manuals to the letter (several times) and I can't quite get the sound that I want.

Is there a general rule of thumb when dealing with so many crossovers?

Thanks

If the speakers have crossovers use them, I am not sure on those amps if you can bypass them or not, if not select full this will let the speaker crossovers do its thing. Headunit crossover turn off if possible. On the sub, i would use the crossover on the amp and set it to LPF maybe around 100hz .