Hi Drew-
No, I dont think you would need to run the aerator all the time. I typically run mine in cycles. You dont want to just turn it on and run it 24/7, it circulates too much water and induces too much chemical change in the water too quickly. What you would do is run it for 2 hours a day, then 4 hours, then 8 hours, then 16 hours, then 24 hours. Continue running it 24 hours a day for 4-5 days, then turn it off for a week. Hope that makes sense.
All in all, you might end up running the pump 1/3 of the time to get your results.
The bottom diffuser aeration does more to circulate your water than to aerate it. Like turning a
compost pile, too much of a good thing isnt a good thing anymore. So circulate some, then let it settle again.
Circulating the water in your pond increases the pond's metabolism, so that the excess nutrients get used up rather than stagnating.
hope that helps, any other questions feel free to ask-