That does all sound possible. If you're keeping the factory HU, you might just want to plug the empeg into it instead of the CD changer. There are a couple companies out there that make adaptors for stock stereos, so perhaps they make one for yours. A seperate amp is actually better sound quality wise, so if that appeals to you, go for it. Many people spend close to what they'd need to spend on an amp trying to get a decent AUX in on their factory head unit.

If you go with the amp, you'll need to get a line level converter for your factory HU, and then one of "the rca switches" that switch between two inputs depending on which amp remote line is high. A competent installer should be able to do this all for you, so just shop around untill you find one who gets what you're trying to do, and why you're trying to do it. Many of them don't deal with RCA switches, so you might want to find that page (crutchfield sells them) and print it out for them.

Congrats on the new purchase.

Matthew