There are some great threads on this topic in Gear & Accessories area, in the favorite and most hated saddles discussions. However, I also had saddle problems with my new Trek...
The saddle that came with my Trek hurt my girly bits waaayy too much. After messing around with the angle of the saddle, height, fore/aft position, etc, I got a Terry Zero X saddle from here on TE, and it immediately relieved the pressure in that area. But, (no pun intended, no really) I ended up with sore spots on my sit bones for the first couple of rides. I think the pressure transferred from one area to another. That, and the Zero has less padding than the original Trek saddle had.
After a couple more weeks of riding, some long and some short rides, I have come to love this saddle. I just had to toughen up a bit on the sit bones.
So... I guess a little more info on where you are hurting will help you determine what to look for in a new saddle. I am no expert, but I found the advice in the saddle discussions very enlightening.