Hello -and WElcome to Koko's!!!
Very smart to have that check valve. As you know, it is a protection against accidental water flowing back into your airpump - something that can happen if you unplug it or the power goes out.
The air flow valve, on the other hand is not bothered by water. It would not be harmed nor would it harm anything if it were to fill with water. So it makes no difference where in the loop you place it. I put them in where ever they are convenient for me to reach so I can adjust the flow easily!