You should probably ignore most of the water chapter in How to Brew. Your water is excellent for brewing (essentially RO water). For most styles you'll just need to add some CaCl2 and/or Gypsum. The water primer thread (http://www.homebrewtalk.com/f128/bre...primer-198460/
) gives general guideline amounts based on the style of beer.
edit: To answer your other questions, the nomograph in HtB tries to calculate how much alkalinity water needs based on assuming the pH of the mash is a function of the beer color. While this is roughly true, beer color is only loosely related to the mash pH and this idea is now somewhat outdated.
If you want to directly adjust your mash pH, then the best way to do that is with a pH meter. The strips generally read about 0.2 low for some reason and aren't too reliable. In general you don't want to add alkalinity to your water (baking soda, chalk, pickling lime) unless you're really really sure your mash pH is going to be too low (most of the time it's not unless you're brewing a really dark beer). If you don't want to buy a pH meter, a spreadsheet like Bru'n Water (https://sites.google.com/site/brunwater/
) will help you make rough estimates of the mash pH given a particular recipe and your water profile. If you do end up needing to add alkalinity, then pickling lime (Ca(OH)2) is the best way to do that, but measure it carefully - a little goes a long way. Baking soda can also be used, but this adds sodium, which is generally undesirable. Chalk won't dissolve unless you do elaborate things, so it's best avoided.
Magnesium should generally not be added since the malt contains enough of this for the yeast.