Hi BJ - just done this in my newly acquired Lunar Clubman. Wiring was all there, but had proprietary plugs for a removeable unit. I just chopped them off, then used a 12v tester to identify the wires - a bit of masking tape and a pen will allow you to note which is which and help anyone else later on. Chances are if you're buying a new stereo the standard ISO harness to the back of the stereo will be included, but if not they are cheap enough from Maplin. Connecting into the existing wiring with Scotchlocks is possibly the easiest method, I know folk aren't keen on them, but if you make a good connection and wrap up in insulation tape to minimise movement, you should be fine.
I had no constant 12v live so ran an additional wire with an inline fuse so the stereo will remember the presets - it's no dramas to re-enter them, but the current draw isn't significant either. If you leave the inline fuse somewhere accessible you can always disconnect it independent of the battery if the need arises.
Use a 9V (square type battery) to identify the polarity of the speaker wires if they are already in place and the wiring isn't easy to identify by looking behind. If you are fitting new speakers, be super careful what's behind where you're cutting and tape over the area you are cutting to avoid scratching the surface.
As an aside, I don't know how you listen to your music, or if you have already bought a suitable stereo, but if you have already converted your CD's into MP3 you can burn maybe 10 albums to one CD saving on storage space. I bought an mp3/wma player from Halfords reserve online for store collection, complete with remote for maximum idleness and paid no more for the extra functionality over a regular CD player. If not, a player with an AUX input for say an IPOD is always useful, you can then run a TV through the speakers if you wanted.