EZ Water won't tell you what minerals to add to your beer because that itself is a fairly broad topic with a lot of opinions, and there's just no easy way to do it in that format.
Here's what I do. For any given style that I'm trying to replicate, say "English Pale Ale", I google "Water profile for English Pale Ale". From there, check out peoples posts on various forums where they'll list their mineral composition. It will usually look something like:
From there, you can open up EZ Water and start putting in minerals. Look at that "Step 5" section in the spreadsheet, and you'll see the beer's mineral profile change (it will match the above format). When you get close to the profile you were shooting for, then you've got it in the ballpark.
Adding Gypsum drives up that SO4 number, while adding Calcium Chloride drives up the Cl number. More gypsum = sharper hop flavors, more Calcium Chloride = more smooth malty flavors. So if the recipe is an American IPA, you know that your gypsum will probably start off higher than your Calcium Chloride.
The addition of acid malt will move pH down without affecting mineral profile, so you might want to leave the acid malt blank, then get your mineral content to match up, then adjust the acid malt to hit the desired pH level.