I only run my aeration system when the air temp is less than 85 F in the summer time. This means a run mostly at night. My system should, theoretically, turn my pond over several times in a 8 hour period. Rule of thumb is to turn the pond over once per day, but if you are not able to run during the hot daytime...now, you need to turn it over in a shorter run time. My guess is that your 2 diffuser system for a 3 acre pond relies on 24 hour operation...that's a guess. Can you come up with a lift rate for your diffusers and how many gallons your pond holds?
Do not run an aeration system during the hot daytime if you need to keep water temps down. I start to worry when the water 18" below the surface (out away from the bank) gets to be 85 F. BUT you need to feel good about turning the pond over enough. I have read that if the pond has too little aeration (read too little water movement) then you will not get enough turnover to overcome the accumulation of toxic water and all you're doing is making the upper good water worse. I have no proof of that, just read it and it make some sense. Too little aeration is worse than too much unless too much aeration leads to a super-heated pond.
The depth at which your diffusers are located dictates how much water movement you get and that determines how many times the pond gets turned over per day. Do you have a thermocline developing? Probably not just yet as you are in startup mode, but you will want to know that.
My gut tells me that you should get the other two aerators and pump working soon, but I can't say for sure without all the specs on the system and volume and shape of the pond.
Too much aeration will effect water temps if your not careful. Beyond that, turbidity could become an issue, but that is debatable.
Here are couple of my threads where I explore and discuss my aeration system with some calculations and such. I think you will find them a good jump start on your quest...http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Main=37540&Number=489945#Post489945http://forums.pondboss.com/ubbthreads.php?ubb=showflat&Main=38024&Number=494996#Post494996
Keep in mind that I am still learning and experimenting with the whole aeration concept.