My bathroom was gutted to the studs. Now we are to the point of mudding drywall. I'm wondering if I need to use red guard on the sub floor and green board (around bathtub shower) before I install cement board. Or do I just wait and paint red guard on the all the cement board once it is installed.
You can do either. Just don't do both.
Behind the cement board is more similar to older membrane systems. On the cement board surface means the waterproofing is what your tile thinset is directly adhered to, which is supposed to be fine, if the backer is correctly primed with the waterproofing compound, but some folks prefer having that attachment be directly to the backerboard with the membrane back one layer.