@amit_mechengg, "Bass : Zero, Treble : +3 , Fad : +2" is not flat - all at zero will be.
"preety flat"

No, she's not, she is quite decently endowed!!!
"The amp is set to LPV mode and not the full mode" - this is OK, you are basically telling the amp not to waste power on mid and hi frequencies.
"subwoofer is
bridged to the amp with
negative grounded": Not understood. "Bridged" means connected to + of L and - of R, and - of R should
NOT be grounded! If you mean - of power supply, I'm not sure if you have +ive or -ive ground in your vehicle. We don't even know what else do you have: HU, speakers, etc.
"the tuner which tunes from 0-6 v ... HU is 45 X 4 watts and the line out is 1.5 volts against the pioneer/ sony 50X4 watts and line out 2.5 V": data not relevant. What IS relevant is that
a. your fader is set to +2 to rear - this should be 0. Come on, you have an amp, and amp GAIN should take care of this
b. keeping fader at +2 you would be keeping the volume higher than normal to get decent volume in front
c. You have not tuned your system well
d. Don't go by 'declared' engineering data, unless you are measuring it properly.
"i dont get the complete punch from the woofer it seems. the woofer is very powerfull. its 250 RMS i.e more than the JBL base tube i.e 125 rms": The woofer
can take 250W rms, but is the amp able to give it? Maybe not.
Post pictures of your installation, so that we are able to relate to it and see if something else is wrong.
Now, try this:
1. Connect the RCA cables going to amp to the FRONT pre-amp out, not rear
2. Set all tone controls flat, set fader to zero
3. Play some normal tracks, which are not bass heavy
4. Keep amp gain at 0 (for the time being)
5. Keep HU volume at a comfortable hearing level (OK, OK, no bass, but still...)
6. Now slowly raise the amp gain till you can just
feel the bass from the sub. Don't look at where the knob is set, unless it already reaches max before you feel it
7. Play a set of bass heavy tracks (drum & bass, for example) and see if the setting is OK. Increase gain if you feel lack of punch. If bass is becoming overpowering when you increase volume, reduce the gain a bit. Set fader to front if the image is too close to you