I would suggest turning the sub down a little. 4 inch speakers are designed to play above 130Hz generally and a sub will happily play everything below that. So they should be able to work in conjunction with each other. If the sub is overpowering then you have either too much bass, or too much resonance. I am not sure the deck but some things to try would be fade the sub a little to tone it down, turn the bass down, high pass the 4 inchers and low pass the sub, sound deaden you car.
When you decide to upgrade I would recommend 6 - 6 1/2 inch splits for the front running off a nice amp. You will get a much better off axis response with splits as opposed to coax speakers.