yello said:Trial and error. Sometimes you just have to tweak saddle positions (up/down, fore/aft) bit by bit and see what helps and what makes matters worse. It's also a matter of getting used to things sometimes. But, that said, you shouldn't ignore pain.
Though I did have an odd thought. You say your LBS fitted you on the new bike, perhaps it's the OLD bike that was at fault and you're just getting used to the new (and correct) fit!
Can you remember having any pains when you first started riding your old bike?
Bill Gates said:rode through the pain.