If you got a stereo with rca outs on the back you just hook up an amp and sub in the boot and run the rca leads to the amp for the sound.
If it doesnt have rca plugs then buy an amp with high level inputs and wire into that. If you get a four channel amp you can run the sub off 2 channels and the rears off the other two channels.
Ask at your local stereo shop they will help you out just dont be fooled into thinking that you need to spend big dollars on an amp to get decent sound.
Most off the boss audio or equivelent amps (around 200$) are more than good enough for a decent sound unless you are doing competition stuff.
Don't listen to this guy.
First of all, he meant to say "head unit", not "stereo". But yes he is correct about the RCA's. To run a sub you need an amp. Amp needs power, audio signal and switch wire. Run power from the battery, RCA cables from the back of the head unit, and a blue remote (switch) wire from the back of the head unit. Then you simply run your speaker wires from the appropriate channels on the amp, out to your sub/s and/or speakers..
If you get a 4 channel amp, which is what most people do on a budget, the common and most effective set up is to run the 2 rear channels bridged to your sub, and the front 2 channels running your front stage speakers. Don't bother amping your rear speakers, especially without your fronts amped. You will only drag the sound stage to the rear of your car and it'll sound like crap. You want the sound up front with you.
If your local car audio shop is Autobarn or Supercheap, then don't bother asking them for advice, they'll only try to sell you their crap BOSS gear. Don't be fooled into thinking a BOSS 1000W amp is going to give you massive power and be so loud. They only give max power ratings, which even then are probably over exaggerated. More often than not, you get what you pay for. If it's cheap, it's not going to give you the power and quality of a more expensive brand. One exception I can think of though is Jaycar's gear. Great quality gear for the price.
Anyway the point is, if you want a decent stereo, you need decent gear. If you buy crap like BOSS, all you get is a crap stereo.
If you can't afford much then just upgrade your head unit for now and get yourself a decent set of 6" or 6.5" splits for up front, and run them off your HU for now. Worry about amping them later when you can afford it, and then add a sub.