BeerSmith does not take into consideration your water profile until you add it to the recipe as an ingredient. It assumes distilled water unless otherwise directed. Once you add your water to the recipe, that profile will show up in the mash tab as the base water under the 'estimated Mash pH' section and you will see a change in the calculation of estimated pH.
Adding any water salts to the recipe will also not figure into the mash pH calculation. The same goes for acidulated malt additions to the recipe.
So, what you want to do is go to the water profile tool and start with your well water as your base profile. Make sure that the water volume for the base profile matches the average volume you want to treat. Make any water salt additions you would normally make to get the water profile you want to build for that recipe. Give this target profile a new name in the section on the water tool for 'target profile'. Click on 'Save Additions to Target' to create a new profile which contains the water salt additions based upon that starting water (base profile) and water salt additions (based upon the volume of water entered in the profile).
Now go back to your recipe and add the new water target profile to the recipe. If you want the water salts to enter into the recipe based upon the water requirements for that recipe, then click on 'yes' when the program asks if you want the water salts added to the ingredients. If you want to wing it yourself without the water salts listed, then click 'no'.
Now the estimated mash pH will reflect the water profile you have added to the recipe.
As an aside, your actual water pH has very little impact on the mash pH. It really determines the species of carbonates which are present in the water which in turn DO affect the mash pH. This does not impact mash pH as much if your water is soft with low carbonate and mineral content, but does make a difference if your base water is high in minerals.
Also if you decide to change the mineral additions for a recipe to which you have added a water profile, that change must be made to the water profile using the water profile tool and then that water added as a new ingredient. You should first delete the former water profile in the recipe so as not to create confusion.