First what amp have you got ?
Most 4 ch amps will let you run 3 ch , as in ch 1+2 on front component duties and ch 3+4 bridged to do sub duties.
You will have more options on the control of your sub by running the dedicated sub line out from the head unit and if you amp has not got a decent low pass filter on ch 3+4 the chances are the sub will play midrange too and may result in damage to the sub and DEF shit sound quality.
It would be worth the extra hassle to run another rca just to get bettersound quality and control from the headunit.