I do water changes in a coupla different ways as I have a some diff types of tanks.
In my 10g planted I use a small siphon. I vacuum up the detritus laying on top of the sand, and usually pull out about 2 gallons (20%). I use 2 clean plastic gallon containers; fill them with tap water that matches tank temp and add some dechlorinator/dechloraminator (I still dunno if that last one is a real word LOL
). And then pour it in.
For my 55g, I could spend hours dragging around buckets, so I got a Python. Its a hose system you hook up to the sink faucet; you can gravel vac/remove water AND add water with it. I gravel vac the bottom of the 55g really well; it has gravel and lots of plec poo LOL
so I really dig into it. In that tank I remove about 30%. When I'm done gravel vaccing/removing water, I match the tap water temps to the tank, and switch the Python to fill. I add the dechlor right into the tank as the tap water is pouring in.
I've never had a problem with either way. IMHO
, as long as you are adding the dechlor along with the tap water it should be fine. Dechlors work instantly, and I doubt the chlorine/chloramine would be in the tank long enough to affect the bacterial colonies.
I would suggest you look into a siphon; by just pulling water out with a cup, you are not getting the rotting food/fish poo out of the bottom of the tank. As that builds up, it may cause ammonia spikes. As long as your tank is cycled, gravel vaccing half the tank at each water change shouldn't be an issue.
Btw, what kinda tank and fish?