I cleaned out my fish tank completely, how long should i wait to put my betta back in?

[♥s my kitty]

So when i woke up i saw my betta with a huge chunk of his back fin gone. So i thought fin rot, and since i cant go to the store i thought i would just clean the tank out completely, to get rid of the bacteria. And after i dumped out all the water in my 5.5 gallon tank. I realized it probably isnt fin rot, he probably bit his own fin. And well now my tank is filled back up, but i used tap water (that way i can have it at 78 degrees or else it takes forever to get there with my heater, its a good heater at getting it at a certain temp and keeping it there but its the getting it there is the hard part) And i put in the stuff that gets rid of the chlorine in the water and all the other bad stuff in the water out. But how long should i wait to put my betta back in. Right now he is in one of those little cups you get the betta in from the petstore. And i dont want to have to wait like a day or two because the temp in the little cup will decrease by then.

I know i was stupid to clean out all the water but it already happened, so please dont give me any crap about that. Just please answer my question of how long i have to wait to put my betta back in.