I am not an expert, but aeration versus algae is a frequent topic on Pond Boss.

I think the consensus is that aeration is NOT an effective deterrent to algae formation and growth.

I suspect the smaller pond being 12' deep has a much greater effect on your water quality.

Do you currently have valuable fish in the small pond? If not, then perhaps you could run an experiment and turn off your aeration in the small pond for a month. Observe the algal growth, and determine if the aeration is a significant factor.

Hopefully some of the experts will drop into your thread.

Good luck on improving the water quality of your big pond!