It's fairly simple. Just select the pledge you want and then when you're checking out, just manually add the amount of the add-on's to the pledge. I.E. If you pledged for the MR. JOHNSON level ($100) and you wanted to go all in on the metal dice, simply add the UPGRADE amount to the MR. JOHNSON price. Mr. Johnson $100 + Metal Dice Upgrade $170 = $270. That's the amount you pledge for!
After the campaign we'll send you a pledge manager survey and you can select the items you want there for checkout so we know what to send you. You can see the FAQ for more information on why it's good to pledge early.