No matter what path you take, expect to spend lots of money minimizing all the prior years of eutrophication that have finally degraded the water quality of your 2 lakes to the point of now having HAB algae. Fixing and dealing with it will expensive due to the total surface area and degree of eutrophication of the lakes.
It will take high pressure compressors to get ample air to the 55ft depth and less psi to put air to 35ft to get the required water turnover per unit of time. I would use the smaller water body as a test subject before spending lots of money on both lakes.
Without knowing the water bodies, I assume both lakes stratify. Hypolimneic water may or may not loose DO in the summer. Deep water aeration will disrupt the stratification, dilute the surface nutrient balance and may or may not help mitigate the HAB. Anoxic phosphorus laden water from the hypolimnion could stimulate more bloom - depending on numerous factore. Depending on the volume of hypolimnion, blending that water into the epilimnion may, I emphasize may, reduce the phosphorus levels enough the HAB bloom will not be as abundant?. What really needs to be done is to sample the nitrate and ortho-phosphorus (ortho-P, soluable-dissolved, bio-available) concentrations biweekly or monthly from May 01 to Oct 01. Analyze the results. If possible the hypolimnion should also be nutrient monitored. Note - Total phosphorus measurements are not necessarily the best indicator of HAB potential. Total P measures all phosphorus including ortho-P plus all that bound as unavailable in all plankton, bacteria, and detritus. Total P is usually several times higher than ortho-P. Some N:P indexes (Redfield Ratio) will use total phosphorus as the P. Total P is often used to gauge or estimate the overall productivity or trophic index of a lake.
I suspect that inflowing water is rich in phosphorus and is feeding a lot of the HAB bloom.
Which lake has the larger area and which one has the worst HAB blooms? Do you know the offending algae species that cause the HAB blooms?
In dealing with this HAB problem explore the cost of trimming and treating the HAB bloom with Pak27 (peroxygen solutions) a fairly new environmentally safe product for HABs used my many municipalities for effective HAB reservoir management. This product requires proper timing, application of the product, proper dosages, and a specially modified boat to effectively distribute the product.
http://www.peroxygensolutions.com/http://www.peroxygensolutions.com/market-segments/residential-recreational-lakeshttp://www.peroxygensolutions.com/purchase/international-other-than-canada Have the lakes ever had a general limnology survey that examined thermocline depth and volume, water chemistry, the nutrient budget, aquatic plant survey, algae - zooplankton survey, and fish survey? All these things enter into rationale of HAB management. Contact the closest University with a good biology department or with a limnologist. The limnology class professor may be interested in making your lake a class project.
I know there are knowledgeable and educated, professional experienced lake managers in Indiana. You should be able to get a list of them from:
http://www.nalms.org/ 
