Is this for 5e? You could track this with an API script like CombatTracker if you need reminding in combat. You could set also their sheet to Query Advantage, which should remind you if they're at 1 or 3 levels of exhaustion to apply disadvantage as appropriate. You could also use one of the token markers like the snail - instead of clicking it, push a number key, and you'll get a handy little "Exhaustion level x" marker. How much exhaustion are you tracking, and is it going to be all campaign? That would probably be the deciding factor in how much effort it's worth going to.
