the PH box is definitely worth paying attention to. if you have a pitcher who is a very good hitter you can leave the PH box unchecked. also if you want one of your starters to always go as deep into the game as possible, it's a good idea to uncheck the PH box so they don't get pinch hit for in the sixth or seventh inning when they're at 70 pitches.
the PR box is pretty much irrelevant for pitchers, it's very rare for it to happen, because if a pitcher is hitting for himself it's usually because he's going to go back to the mound the next inning.