Does the ledger board for a bathtub go under the flange or level with it?
Your tub should have clear and specific instructions. It varies by model and material.

However, if a ledger board is used, it'll be under the flange, providing support from below. There's no point to a ledger if you have a typical framed wall and can simply nail the flange to the studs every 16". 

The only tubs I've ever installed using a ledger are large spa-type tubs, and those are usually set into a full deck. Typical shower tubs simply get fastened to the wall framing. Do follow the instructions, though, or you'll void your warranty.