Go, go go! Rule of thumb is: if it hurts, then get a certified lactation consultant (IBCLC). Your nipple should not be flattened, should be pulled out by the baby's suction. There's a vicious urban myth that latch should hurt, and while some initial discomfort can happen, further discomfort and especially pain should be checked out quickly by a professional.
I tend to be a bit aggressive about this for a few reasons, first, because my DS was unable to create suction (a question of technique, not anatomy) for a couple of weeks. It meant weeks with a breast pump, supplementing with formula, Reglan to increase my milk supply, etc etc etc. But I've seen the effects of a trained lactation consultant in action, not just for me but for others: if called upon fairly quickly, they can work wonders. Some people also find a local La Leche League leader helpful, but I personally tend to start with the IBCLCs, if only for their clinical training. My bias, admittedly, was shaped by my mother, who is a long time member of LLL and LLL leader, and is also an IBCLC.
Best of luck to you, and I hope the resolution that you come to works for you and your baby.
-Ziva, wife to Ezra

: , SAHM to Elisha

, mama in waiting to a new baby bean, ODD 9/13.