Do I count the time getting the food back to temp?

When the water is preheated, naturally the temp drops from putting food in. However then the app doesn’t start the timer until it is back 1 or 2 degrees. Should I just use another time and count the time with food in, just a few degrees shy? Or should I wait till it is completely preheated and go with the app timer?

 I wouldn’t worry about it and just let the timer start when it comes back up to temp.  I can only think of a very few things that you could cook sous vide that would be affected by a difference in cooking time of a mere couple minutes. 

I just drop the food in during the preheat and then I don’t have to touch it.

A few things like eggs are time critical. Everything else cooking for a few extra minutes no real impact. I typically add my food sometime during the preheat and by experience I know how long it will take to reach the proper cooking temperature. I also start out with hot tap water to reduce the time.