Are you adding stress coat just for the amount you are refilling or for the whole volume of the tank? when you are refilling directly from the tap instead of pre-treating, you need to dose for the WHOLE tank. also, are you leaving the filters running when you do the water changes? the bacteria can survive a good 30 seconds of contact with chlorinated water, but past that they'll die. and in that 5 minutes, you can also be harming the fish. you don't have to "devise" a way to treat the water first, you just pour the dechlor into the tank itself. that way the chlorine is almost immediately neutralized as soon as it comes into contact with the dechlor chemical. if you leave the filters running when you refill, then the chlorinated water is going into the filters and killing off the bacteria there too.
would you rather go into a room filled with poison gas with your gas mask on already, or have to hold your breath and put it on once you were already in there? extreme example, but same point. Chlorine is a poison. Dechlor is your fish's (and bacteria's) gas mask.