FWIW, I use Bru'n Water and I also use acid malt for any situation where I need to lower mash pH. When I plug in my grist in Bru'n Water, I simply omit the acid malt. Then, I just add acid malt to lower the pH to my desired target. I use the Weyermann rule of thumb that Martin mentioned, and I've never had an issue. For example, yesterday I brewed a pilsner for which Bru'n Water projected a mash pH of 5.7. I added 3.2% acid malt to the grist and my mash pH was between 5.3-5.4, which was my target.