Sounds like a plan to me.
We've been using cottonseed meal to fertilize the ponds this spring. We're still leery of liquid fertilizers and the quick/heavy bloom they can produce. The cottonseed meal, added a few hundred pounds at a time to a 4 acre pond, seems to give us a slower, steadier bloom.
At any rate, you're a pro at this, so I'm sure you'd be fine with the liquid as well. I do like the idea of applying some to the bottom first, then letting the pond fill
How big are you browns compared to the brooks? Are they basically the same age?