I've lately been mashing all the base malts, adjusted to proper pH with acid, capping the finished mash with crystal and roast malts if any, then adding salts in the kettle, like Denny suggested. I add a little acid to the sparge water so the mash pH doesn't rise during sparging.
I wondered recently if I could add the salts for flavor after I had the beer in kegs. This way I could make 10 gallons of pilsner, then turn half into a Dort Export with salts.
Flavor salts work with food......