Wow, some people tend to overcomplicate things, IMHO.
All I do is annotate the CR's number and inning right next to name of the current F1 or F2 (and not in the "Substitutes" column of the lineup card). For example:
#8 F1 SMITH, B.
CR12(3)
#2 F6 WALKER, R
#6 F2 JONES, J.
CR16(4)
This means #12 courtesy ran for F1 in the third, and #16 CR'ed for #6 in the fourth. I don't use the back of my lineup card for anything.