get he RCA's happening asap.

Shielded cables will prevent unwanted noise entering your system and 3.5mm cables wont be shielded very well compared to good quality RCA's.

More than likely you will have to run a ground loop isolator due to poor grounding of your computers motherboard.

BTW, i also recommend running your sound through a head unit.

I've done it both ways, and just preferred using the head unit as the audio controller (analog-ally) rather than using the computer.