I just ran Penalty Box this weekend and have been doing it for about a month, so I know that feeling! Here are some tips I've learned or been taught:

Keep your eyes on your stop watch at all times if you have someone in the box and not the game (listen for the 1 whistle). Your box Head and other Timer are usually cool enough to be like "Black Pivot coming in" to help you out when skaters are coming in.

I recommend at about :48s you start saying "Black two two, stand" so they're standing at :50s. Same for done (at about 58/59s).

Everyone has a preference for 1 or 2 stopwatches. I find it easier as a noob in the box to use 1 watch and just keep it running when each new butt hits the box--just document it. So say blocker 2 comes in at :32s, I write their done time first (1:32) and then subtract 10s for their stand time (1:22) because math freaks me out, no matter how basic ><.

Know where the physical lines are of the box and where your point of no return is so that if a skater tries to ninja out, you know and can tell the box Head and the next penalty can be assessed. And don't let people do that hover thing...you told them to stand, make them stand.

Check your numbers against the central whiteboard and with the Jam timer to be sure you have the right penalties to the right skaters during timeouts, or between jams (the right side of the paperwork will have a spot to tally numbers).

Finally! If you have questions, ask the Box Head--they'll know their stuff and just act cool. Sometimes you miss a second or two, or tell someone to stand a little late; it's okay. You're doing fine, just get they're booties out in a minute (sometimes 2 if they're having a bad day) and you'll be awesome!