Air filled PVC under the water will easily lift itself out of the water, even buried a foot or more. Use the self-weighted tubing anywhere lines go under water. I think you will need 2-3 pods of 3 9" diffusers in pond A and only one, 2-3 diffuser pod for pond be, at the deepest point.

In pond A, I would place one diffuser pod a little south of the current pond's southern extreme, or the center of the wider part depicted in the future water lines (in 9' of water), one pod in the deepest point, and one pod in the current pond's eastern point in at least 9' of water to move water as far into the future eastern cove as possible.

Place your air valve manifold where you can see all diffuser so you can "balance" air flow to each pod.

With a total of 4, 3 diffuser pods, you will need a minimum of 5CFM flow at 7 PSI to supply all the diffusers. If you cut back to 2 diffuser pods, you will need 4 CFM. I don't believe single diffusers will move enough water to turn the volume each day at least one time in Pond A, but might in Pond B. Membrane diffusers need a minimum .5 CFM (max is 2.5 to 5 CFM depending on the diffuser brands) to operate properly.