I'm not sure what you mean when you ask, "how many staples in a row at 12 inches" You can staple the paper as much as you want, so to speak. BUT, if you put in too many, the paper won't have room to 'shrink' when it gets warm, thus, allowing the shingles to lay flat. Sure, it's OK for the staple heads to show. You're going to be covering them up with shingles. It's the SHINGLE's NAILS that you DON'T want to show. Because, if they do, you'll most likely end up with water in the house! IF you have a situation where a nail shows, just buy some clear 100% silicone caulk and caulk over and around the nail/staple about 1/2" area on EACH side. Use your finger, or a piece of plastic, to lightly 'press' the caulk down. Remember, there are granuals on top and you don't want the caulk to just 'sit' on top of them.
If you need more info, Post up or e-mail me directly. (Your Post is starting to get 'buried' ...)