I'm trying to decide on a drainage system as well for this entire system. My current project that requires water from this cistern is my sewer system that will allow for a well in every dwarf's room. With that said, if I needed to drain said sewers, my original intention was to simply pump water from the sewers back into the top of the cistern and thus completely fill the cistern back to its original levels. I realize though that there is no way for me to be able to pump every single unit of water back into the cistern and that instead there would be quite a bit of shallow water that would just evaporate.
I build only close-circuit systems, with water circulating and being reused, though it needs to be partially refilled sometimes (depending on system, like once or twice per year). I also make wells within these systems. Both wells and splashes of water (1/7) make some water disappear after time. Shallow tiles will evaporate randomly, but if they are low in water only for a limited time they usually won't evaporate before being wetted more, to 2/7 or higher level. I'm not sure what algorithm is used for evaporation, but it seems it's similar to radioactive decay (exponential with a set probability) so the last wet tiles can last for quite a time.
I'm not sure what is your intention - to clean dwarves (which will remove traces of forgotten beast extracts or blood) or to make them happy, but wetting dwarves is not enough to make them happy. They need mist, which assumes there will be some losses in water. And mist can be created on different surfaces, but grates seems best for it. Grates also decrease (or nullify) pressure, like diagonals.