I have pretty boring water, really low in Cl and Ca, so I am adding some chalk, baking soda, and cacl for a wee heavy. My water has a so4 of 62, and cl =24, and an ra of 88. I'm making the traquair house clone, so i really want to get the cl:s04 ratio up as well as raising the RA a tad. So I guess since I am wanting to effect the pH I would add to the mash.
Tha is a good point about the gypsum though, no sense in adding it to the mash if you dont need any pH/RA changes. I will definately keep that in mind for future brews.