There are always 2 sections with bubbles. They will only respawn at a different section when ALL bubbles in another section have been captured!
If there is seemingly only one section with bubbles, there is probably a golden one left somewhere...
Each golden bubble is good for 5 points.
The Puncher section is the best to get individual bubbles but its golden is pretty hard: you can get it by jumping subsequently on the same spot or by jumping on another bean first
I like to go around and enter the puncher section from the back where you'll have more chance for uncontended bubbles.
Even when doing horribly (3 beans qualified, 2 bubbles collected), the punchers can get you back on track swiftly