First, let's understand what the pH reading of your water tells you (and the software). The pH reading determines the species of the main buffering component of water: the carbonate ion. The carbonate ion can be found in 3 different forms in water, H2CO3, HCO3-, and CO3 2- and the balance between the three helps to determine the pH of the water.
The amount of buffering is then determined by the total amount of carbonate ions you have in your water. This is usually supplied indirectly from your water report as ppm of Bicarbonate. [note: I don't have a Ward report in front of me, so I cannot remember how they typically report it.] The software uses the pH to determine the amount of each of the carbonate species to calculate the effect of the natural pH contribution of each of the malts has in combination with water ions to calculate the pH of the water when the malts are added to the water.
The effect of further addition of salts will be calculated in to come up with an estimate of what your mash pH will be. If you want to lower the pH, you can add Gypsum, Epsom salts, or Calcium Chloride to lower the pH and/or Chalk or Baking soda to raise the pH. Alternatively, you can jump straight into addition of acids or alkali such as Lactic acid, phosphoric acid or pickling lime (alkali) to control pH.
You can open up the BeerSmith water tool and either make the additions manually to see the outcome of the water ion balance or plug in a target profile and click on 'match target profile' to let the program determine the salts needed to be added to reach that profile.
TL
R - Don't sweat the water pH, it is the carbonate ions and malts which will determine the initial the mash pH.