Glad the fish are feeling better. If you are going to be watching the tank go ahead and take the powerhead out, you can turn it back on if you see the fish going to the surface again.
Prime is only dosed with new water that has chlorine or chloramine in it. It can affect oxygen level too and tap water itself can be low in oxygen. I always aerate replacement water at water change time now after a couple times the fish were uncomfortable after water changes.
Dose the Flourish as directed. It helps the plants grow and doesn't change how algae grows, algae can always find nutrients.