Well, I think, I don't need to change the Head Unit to achieve the said setup, since its a 4-channel HU. 2-channels are being used by 2 speakers. Other two channels can easily be used by the Amplifier by bridging and the amplifier then can provide output for the subwoofer. The amplifier is modern enough and can easily handle Speaker-level input. I agree that this Head Unit (DEH-2950MP) doesn't have controls for subwoofer, but I don't need them either. The Amplifier itself have a Remote Control for gain adjustment.
Totally agree to you. For now, the setup would be great (I was only worried about the effects on battery, which I think won't be any).
The subwoofer's R.M.S power input requirement is 400W, and the amplifier's R.M.S output power is 300W@4ohm, so its a good match. I believe better not to over-power the subwoofer (reasonable under-powering should be okay).
And yes, I will change the Head Unit later when I have more money. 