Ryan, that is true as to fountains. As aerators, fountains do a pretty poor job, but look nice.
If you have cold spring water that flows over rocks and into your pond to aerate it well, I would go with the mid-level placement or fountains as well. If this is not the case in your pond, during the summer months, the cold water beneath your thermocline is a dead zone until the Fall "turnover".
Placing the diffusers at the bottom will allow upper waters rich in dissolved oxygen to be drawn to the bottom while lifting the lower, oxygen deprived waters to realease the toxic gasses dissolved in them and to take on oxygen.
This will raise the temps in the bottom layers, but diffusing during the night only will lessen the rise in bottom temp.
