Kicker KS65.2 flapping bass

hi all. ....

im a beginner installer i have moderate experience installing car stereos (nothing fancy, just speakers, head units subs and amps) and finished my own car last night ...

i installed the following parts:

Alpine CDA 9807 HU (50 W x4 max)
Pioneer GM-X944 Amp (75 RMSx2, 250 RMS x1 (3+4 bridged))
Alpine Coax 2 way SPS170A Front Speakers (40 RMS 200 Max)
Kicker KS65.2 Rear Shelf component speakers (75 RMS 150 Max)
JBL GTO1200 Enclosed Sub (250 RMS 1000 Max)

Head unit amp powers the front speakers, rear and Sub RCA connected to the Amp, channels 1 and 2 connected to the Kickers, and channels 3 and 4 bridged running the JBL Sub

However,

All sounds nice, of course the Kickers are MUCH clearer than the Alpine speakers, but when i raise the volume the Kicker speakers start flapping with the bass and I have to raise the HPF level on the amp to fix it. is this normal or is there something wrong with the speakers? or is the amp giving too much power?

Also I have a Pioneer 2 channel 40 RMS x2 Amp, is it worth it to connect it to my front speakers? or should i leave it as it is?

Also, i understand that to tune a system correctly i should turn everything down then start turning up as much as possible starting from the head unit, and then raising the gain on the amps as needed, but i find that i must turn the gain waaay down so i can turn up the HU up to 35 (the max volume) - is this right or should I leave the amp at normal gain and be careful not to turn up the HU past 24 or so ...

Also regarding the Sub, the head unit gives only low frequencies to the sub channel, I currently have the LPF off. Should I turn it on to further filter the bass or leave the HU to send the right frequencies?

Sorry for the many questions but i live in Saudi Arabia and there are very few professionals here and none are very cooperative and Im finding it hard to get good help

Thanks a a lot

So you have the front Type S speakers powered off the HU and the rear Kicker speakers powered off the amp?
Why?
I would definitely power the front speakers off an amp before the rears.

Yeah the Type-S spkrs are running off the HU.

Switching the Kickers to the front is not really an option as the car I have now is not permanent so i wouldn't want to open up the door again, plus the speakers in the door (the Type S) are relatively deep, and a shop made me a custom bracket so the speaker doesn't stop the window opening. The Kicker speakers are also deep so i would have to make another custom bracket.

thanks for the info on the HPF freq., i'll try that later today and i'll add the amp to the front. Also that means I can turn off the internal HU amp (and use only RCA preouts), which the manual says should make sound quality better as less heat is generated and less power is consumed.

i'll post late and tell you how it all works out