Heuge, I would go with option 2 (rip out the existing stereo and just use the empeg and an amp).

If you went with two head units, you will come to realize (as many others have) that the second head unit is a waste of space. You will hardly ever use the head unit to play CDs. So for the few times you want to play a CD, just keep a cheap portable CD player in the glove compartment (with the correct cables to go to the empeg's aux-in). I do this, and the CD player only gets used about once per year.

If you're worried about having only front and rear outputs, don't be. Remember that separate subwoofer outputs didn't start getting added to head units until recently. And many head units still don't come with separate subwoofer outputs. So what do other audiophiles do without six outputs? Exactly what's illustrated in that FAQ entry. It's really no big deal, and very easy to do.

Remember that a separate subwoofer output is only a convenience feature. It lets you change the level while you're driving, that's all. I have the ability to control my subwoofer's volume seperately from the front/rear speakers, and I never use it. All of my levels are all set exactly where I want them, and I never need to change them.

Also, as you've already surmised, you'd have less trouble with heat for the empeg this way. CD head units get HOT, especially when you're using them to drive your speakers, and there have been a few stories of overheating empegs even when the empeg is mounted below the head unit (because the head unit blocks the empeg's top air holes). You could always install a fan in the empeg, but that's a hassle.

Seriously. Do it right. The empeg works great as your only stereo. And if, after a while, you decide you really want the second head unit, then you can always buy one and put it in.