At one point I had Bubble Algae REALLY bad, I didn't even like looking at my tank. There were thick sheets of solid bubble algae. Read my post at the bottom of this thread, How can I control Green bubble algae?
This is how I got rid of it and it never came back. I wouldn't worry about the few you popped underwater. I think the link that Melosu posted was what I implemented.
180-gallon acrylic mainly SPS, SWC 1A Cone Skimmer, APEX Neptune Controller, 3x MP40w Vortechs, Tunze 6045, Radiums 250w in Lumenarc Minis, Galaxy Ballast, BRS Dosers