I guess first and most importantly: did you get a professional fitting? If not- get one. If so, then it's just a matter of getting used to the aggressive position.
What is so uncomfortable? Neck? Hips? Back?
Every spring I need to re-teach my neck to be comfortable in aero position. It's a slow process (for me), but eventually those neck muscles get strong and it's easier to be down in aero. It's a very different position, so give yourself some time to adjust.
When I first got my tri bike, it fit like a glove and it was love at first ride. My body LOVES that position (with the exception of my neck, who learns to love it).