You can do either. Fondant right from the mold will take the shape of the cake better-if, for instance, it's going on the side of a round cake.If left to dry for a while, they will be more sturdy and easier to work with.
I use Duncan Hines, and they did the same thing. The box went from 18.25 oz. to 16.5 oz. I just bought an extra mix and weighed out the difference. The 1.75 oz difference made about 1/3 cup. Now I just keep an extra opened mix in a plastic container and dip out 1/3 cup to add to the box I'm mixing up.
I always overfill my pans so I am sure to have the height needed. However if by some fluke I do not get the height I need I use the Wilton plastic pillars that can be cut with scissors; they fit into the plates very well. (The SPS pillars are a little hard to cut.)Leah_s has a sticky here on CC that gives great info on how to use SPS.