Let me see if I understand the problem/situation...
As I understand it, the bubbler should run for the day cycle (12-14 hours summer, less in winter) same as lights. So you want the bubbler on while the lights are on. Do I understand you? Are you able to do this? A simple Radio Shack timer will do this.
The air stones need to be "off" at night to lower humidity a bit. Yes, you need them covered with water - I suggest RO or distilled water. If there's some way to run a fan (even manually) at night - or better yet, 24/7, that would be great. There are lots of cheap 12 volt 3 1/2" fans out there like
Coralife 3-1/8" Cooling Fan Kit
My setup is a bit different from what you describe in that the misting system runs during "daylight" hours only, as do the lights. The inside fan, however runs 24/7 to keep fungus at bay at night. A "bubbler" should work just fine to keep up the humidity.
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Ross
http://orchids-ross.blogspot.com/
I don't do most Dendros or large, "floofy orchids". For me it's minis (like Angraecoides), Masdies, Paphs, and others that crept in somewhere along the line. See my orchid list for complete collection (usually not current.)