When I know have to move the bubble, I usually disturb it - move it, shoot a blast of water at it or something to initially irritate it. Then, I usually pick it up by the base and hold it against the glass with light pressure on the bubbles - enough pressure to help it get rid of the water but not enough to pop them. I only do this for short periods of time. I also shake it gently. Once about 75% of the bubbles are deflated, I start checking to see if I can remove it by the tank - to do this I just start trying to take it out of the water upright, if I feel that the bubbles are really sagging, back into the water to let it expel more water.
As for popped bubbles - put it back in prime conditions and it will be fine. I have popped some before without even noticing any ill effect. If you popped a ton, I would just keep an eye on it and make sure the flow is not ripping the deflated flesh from it as Bcollins said above.
Good luck!