Congratulations on a quality setup
Sad to know that you have run into problems right from the beginning, but dont worry these things are the bane of any audio system and can be fixed, they just take some time to fix.
Right then,
Even when a system is installed by a professional installer, there always is a room for error, and it isn't something to get upset about, these things just happen.
Ditch the high level input (speaker level input) and use RCA interconnects to connect the HU to amp. Speaker level inputs are really not a good idea as they always have some level of filtering applied to them which cannot be bypassed plus they filteration is volume dependent, all that to prevent the stock speakers from distorting. Also because they are driven by the HU amplifier, they can and do tend to distort way before the actual speakers and amp can go into clipping. The Best thing to do is to use RCA and feed the amp with a full range signal.
secondly, turn off all the filters from the HU and use the crossovers built into the amp or vice versa, use the HU filters (crossovers) and set everything flat or full from the amp ( I prefer the latter) That gives you the ability to tweak the settings from the HU on the fly. But of course to do that your HU needs to have those options. If not, stick with Amp's filters.
The most important bit is to recheck the speaker connections/wirings. Check weather they are connected properly and in correct polarity ( + to + and - to -) I suspect that one of the midbasses is running out of phase with the other due to reverse polarity. Do check all connections,...each and every one, the tweeters, the mid basses, the rears and the subwoofer. Installers can easily overlook the polarity verification.
you mentioned [I]"He set front fader for all 4 speakers and rear for the sub on HU"
[/I]It seems that your headunit doesn't have a dedicated subwoofer output. Do correct me if i am wrong. If you cant verify that for yourself then please post the model number here, will look it up. Just use y splitters on the front rcas (at the amplifier end) and supply both the front and rear channels on the amp with the front preouts from the HU. And supply the sub amp with the rear outputs.
When you are done with the speaker checks and everything is playing what it is supposed to , then if you find the sub doesn't blend in the with the midbass properly, try reversing the speaker wires for the subwoofer only and try again, one of those ways, the bass would feel louder and better defined.
And please allow some break in time for the speakers, and during the break in period don't crank the volume too much.
Do report back with the results. I hope your problem gets sorted.