You don't change all of the water, and in fact should not. Different people will have different thoughts on how much and how often to replace some of the water but here is the basic consensus:
Do a 15-25% water change every 1-2 weeks. Depending on your bio lab and type of fish you can refine these guidelines (if you list them it will help).
It's very important that you use a gravel vac, which can be picked up for pretty cheap at your
LFS. This will pick up all of the excess food, fish poop and other various stuff that ends up in the gravel. If you don't do this the material will build up, look awful but more importantly will cause water quality problems.
As for the evaporated water, if you're water only contains chlorine and not chloramines you can just leave some water out for 24+ hours and then use it to top of the tank. You can also just treat the water like you would the other water.
I'm not sure what chemicals you're using, but many here would tell you (and I don't use) and stress coat chemicals or anything like that, but who knows? The only chemical that many people use is something to get the chlorine out.