[gunbir]

prashant, I'm assuming you have gone through the glossary and know what HPF/LPF means.

Now, your HU has one HPF setting for front AND Rear speakers. That poses an issue. Your front speakers are 4" while your rears are 6x9s. The problem is that the rears can take more bass then the fronts. So if you set HPF considering the rears (say 80Hz) the fronts might distort. And if you set HPF considering the fronts (say 100 or 125Hz), you will get no usable low bass output from your rears.

I suggest you run the 4" components off the amp. If you are already doing this, then set the HPF at the HU to 80Hz and the LPF to 80Hz as well. On your amp, the channels used for the front comps will have a HPF as well. Enable that (may be set to bypass/off) and set it at 100Hz or so.
On the other set of channels that are running the sub, let the filter be on bypass/off.