I helped a friend put his empeg into his TT - and my opinion based on that is simply to have as little of the factory system installed as possible. If you plan on doing other work, such as adding the empeg and the subs, you'll find that you need other aftermarket components such as amplifiers, etc. None of this stuff plays nicely with the factory Bose stereo. So if you plan on upgrading, don't spend any money you don't have to.

We did manage to get the empeg working correctly, though it took a lot of toil and trouble to do it. It's the only change he's made, so it's running through the factory "premium" system. I won't knock it too badly, since it sounds better than my Mitsubishi's stock system, but I still thought it was only so-so overall. I'm not sure how any company gets away with calling their stock system a premium system.

So again, if you plan to upgrade any of it, just expect to do all of it, at once. Save all the purchase money that you can to get it done correctly somewhere else. Of course this will depend on your plans - forr example if you plan to lease the car you may want to skip the aftermarket setup alltogether. But if you plan to keep it, I'd recommend what I did with my new Eclipse - within a week of owning it I had the whole interior torn apart and I replaced 100% of the stock sound system from scratch.