There are a few ways to to it. I generally mold the liner first, padding for unique features of the foot as needed. Unless they are extreme, the Intuition liner molds right around them.
Did your bootfitter ask about toe caps? I always recommend toe caps to my customers. There are several different sizes to choose from. The other night I molded a pair of Intuitions that were in Krypton Storms for a gal who works in our shop. She was running a full race fit. It was the snuggest race fit I've seen in a while- for JH that saying a lot. She was complaining about toe room, but the standard toe caps did the trick. She now has plenty of toe space.
I'd try molding first, then shell work later.