At this stage, you have a couple of choices.
One thing that appears to be missing is a moisture barrier behind the HardieBacker. When building a shower surround, you have two ways to manage moisture, you either put a moisture barrier behind the boards on the studs and lap it over the tiling flange, or you put waterproofing on top of the wall board. If you don't want to take all of the Hardie off to install a moisture barrier (a sheet of plastic or roofing felt is usually used), then, you need to deal with surface waterproofing. There are a couple of different methods:
- a sheet membrane, sort of like wallpaper
- a painted on waterproofing material
If you choose a sheet membrane, the membrane itself will take care of your CBU (cement backer board) joints. If you want to do a painted on waterproofing, you must use a special alkaline resistant mesh tape on the seams and use THINSET, not drywall mud...let that cure, then add the painted on membrane. That tape may look the same as drywall tape, but it is not...it must be alkaline resistant, or it will disintegrate over time in the mortar. Hardiebacker is VERY thirsty, and if you don't wet it down first, it will suck all of the moisture out of both any thinset or the waterproofing membrane and make further installation difficult. It's not too wet unless there is actual liquid water on the surface...saturated is fine, dripping is not. This will make a HUGE difference in how easy it is to deal with.
Pay particular attention on the tub to wall sealing of your moisture control.
Should you want to go with a sheet membrane, one company that has good products and excellent videos to see what I'm talking about, is
www.schluter.com . Should you decide to go with a painted on waterproofing, RedGard, Aquadefense, and several others all work. While it might seem easier to use a painted on membrane, I think it's a little harder to ensure even coats without runs or pinholes; plus, you have to prep the area first by taping and thinsetting the seams, and waiting at least a day before you can paint on the waterproofing (you have to wait in between coats of that as well).
Pay particular attention to the niche you created. The cement board is NOT waterproof, it's just not damaged by being wet, and it is a compatible surface and stable for putting tile on top of.