i have one question for you...are you wanting to play your ipod through your car stereo? if so then i would suggest a new deck with an ipod adapter. both alpine and pioneer make decks with this, and the sound will probably be better than using an FM modulator. as far as what things to get:
speakers: components have three main parts. the wwoofer, tweeter, crossover. the tweeter and woofer are seperate and are usually mounted close to each other. there are also coaxial speakers, these have the tweeter and woofer mounted together (essentially, you put the speaker in the original whole and that's it).
subwoofers: these are the things that go BOOM. depending on how you want it to sound, it can get real loud and sloppy, or really tight and accurate. some of it depends on the box/enclosure you are using. a ported box (one with holes) will sound more boomier and lose some accuracy. a sealed box will sound more accurate but not quite so boomy.
as far as brands are concerned, it really depends on what all you want. with your budget you can probably get a pretty nice setup. you can ask a million people the same question, "what brand should i get?" the only really good answer, "go listen to stuff and see what you like more".
hope this helps you to some degree, ask if you have more questions.