As far as humidifier water is concerned, I use distilled water. I top it up every day and empty it sometime (when the idea strikes me at an opportune moment).
I agree that pouring leftover distilled water back into the bottle/jug is not a good idea. Leaving it in the humidifier tank is not so bad. The opportunities to pick up contaminants are few and I have never had a problem with it. I will tell you that I have not had an illness of any kind since I started CPAP 5 years ago.
In the end, you should research the action yourself and do what seems best for you.
I use distilled water and add some if it gets low. After four or five days I wash the tank in soapy water. I never pour water from the tank back into the bottle. I know that in some areas distilled water is harder to get or expensive. Here it's only 88 cents per gallon. When we travel I sometime use bottled drinking water.
"Sometimes the magic works . . . and sometimes it doesn't" -- Chief Dan George in the movie Little Big Man