Rock first, so it rests firmly in its final place, sand second, aim for 1.5-2", then finally add water. Try to do it all in one shot if you can.
If your rock has been curing in total darkness, there shouldn't be any growth on it. At least from what I've noticed in my own tank. The cure simply allows basic bacteria to break down phosphates and coat the rock with a beneficial film that will aid further colonization and prevent harmful bacterias.
So back to your question, as long as you can get the rock submerged before it dries, you should be fine. This may mean you have to add rock as water permits tho. i.e. don't add more rock than the current water supply can cover.
Also! If you haven't already, be sure to calibrate your Refractometer with calibration fluid, and not rodi. I just read some serious articles on why calibration via rodi is super bad.
http://www.reefcentral.com/forums/showthread.php?t=1963296
Here is a wicked useful thread on that
How big is your tank? And have you planned out your possible aquascape yet? As in height and width in relation to the volume of water it takes to reach said height?
All in all, you're doing great, just be sure to keep reading, and ask whenever you have a doubt, and even when you dont.