I love keeping score
On your first question, I do one thing different from most in that I just use lines to show if it was pop-up or line drive....
__
3-DP1
would represent line drive to first base in the score box for the hitter (a rainbow line over 3 would mean it was a pop-up)
In the score box for the runner, it would say
3-DP2
I started differianting between when the out occurred because while I kept the book, my husband who couldn't attend many games scored them into the stats program and he needed to know the right order and I couldn't always remember....and sometimes it is not obvious.
As for your second question, I do the same as Fungo writing Balk, WP or PB above the line drawn between the bases shwoing the advance.
Other notes include E-6T for a throwing error by short or perhaps E-3C if first did not catch a throw.
I would draw a circle around the event to show that it effected more than one runner/advance(that is, both runners on 1st and 2nd advanced so the one of the two entries is circled to show it happened on the same play. A two-base error would get the same treatment)
We'll have to figure out how to do notations here.....in score keeping, a picture is worth a thousand words....and a whole ballgame comes to life on the paper