An advanced brewer friend of mine came over to observe my brew day and one of the pieces of advice he gave me was to start adding some salts to my water. Mostly NaCl for flavor, and CaCl to balance to chloride to sulfate ratio and add calcium.
I am adding a very small amount of Calcium Carbonate to my dark beers (1/2 teaspoon for 3 gallon) and a small amount of gypsum to my hoppy beers (around 225 ppm, 1 teaspoon for 3 gallon).
Everything I've read about adding salts to extract beers says to not do it. They say the water where the extract was made has minerals and the brewer adjusted pH in the mash already. I don't doubt that part, although I think the suggestion to me is based on flavor rather than pH.
I've downloaded the Bru'n water spreadsheet and I'm still playing around with it to figure out how it works.
For what it's worth, Portland Oregon has very clean, super soft water. All the minerals are under 10ppm (which according to John Palmer is "damn near distilled") so maybe accounting for the minerals in the extract it could still use more? A typical recipe for me is usually 4-6 pounds of LME and 1/2 to 1 pound specialty grains.