Pads wont last long on fubar rotors.
That being said,remove one pad, replace it then pump up brakes. Replace next one and so on. This way you minimize the amount of fluid displaced back to resevoir.
Theoretically you shouldnt have a problem with fluid, unless it was topped off as pads wore down.
All new pads and new rotors reservoir filled then it should never need topping up. Low fluid indicates worn pads or a leak.
a goood mathemagician could calculate the volumes of calipers and resevoir and have an indicator when pads need replacing, that is if they all wear evenly.