The water chemistry section is loaded from the top menu --> 'Recipe' --> 'Water Chemistry'. It loads a sub-window.
The top section is where you load the water you are using and any minerals, the bottom is for your desired water profile.
As you add minerals to the top window and adjust their amounts you will see the little jewels or whatever they are moving around. Green is a good match, yellow is not that great, and red is normally off further than it should be.
I added two water profiles to my Water collection - my local tap water, and RO water. I am in the process of adding the profiles from Bru'n Water like 'Brown Balanced' and such, since I use those most often.
The thing I can't seem to figure out is if you can get the mineral additions into your recipe. It seems, so far, that you have to note them down manually when creating your brew-day notes. Annoying to me.
The program is the best I've seen at dialing in your equipment, but it's missing a few other nice tools.
Anyway, hope this helps!