Dave... bring the green board down to the top of the base... actually butt the board right down on top of the base WITHOUT overlapping the edge.
Then you will fill the VOID left between the board and the base with a thinset mortar which helps to reduce wicking in the future.
If you bring green board in so it overlaps the base edge it will cause a bow in the bottom of the walls you will be installing soon.
Other choice is to fur out walls a 1/2" and then can overlap base, but you will still keep it at least a 1/4" off the base and fill with thinset mortar, etc...
I usually just butt down on top and fill joint... this also effectively LOCKS the base in place all around perimeter edges! Base will never move!
Good luck on the cutter... plumbing supply will have it or I'm mailing one to you on Monday afternoon... ;)
Talk later...
MARK