IMHO-
I would paint the wells first- then mask them with something known in the states as BlueTak (when I was a kid it was known as FunTak) It's a putty like substance that doesn't harden and has NEVER lifted paint off a model. It wil allow you to mask off the edges of the well no matter what thier shape is. Then shoot the underside.
I would use white as a base for both the yellow and red sections, but I'm not sure how dark of a red you are oing for. (the white under coat will produce a much brighter color)
Hope that helps,
J