Since you have a tuner module, I highly recommend you go with the empeg as your only stereo and use the tuner module.
It is the cleanest install all around this way. It looks the best in the dash, because the empeg has cleaner lines and integrates better into the consoles of most cars than the gaudy aftermarket stereos do. Fewer components means less chance for noise. The anti-theft feature of removing the player from the car is better when there's not another stereo sitting there waiting to be stolen.
You will not miss the CD player. I know that doesn't sound logical at this time, but trust me on this one. Others on the BBS will back me up on this statement.