It makes sense for personal scripture study to be, well, personal. I got Super K into marking his scriptures a few weeks ago by telling him which verses he would read, and how I thought he should mark them. It was a great start, but as a parent, a little high maintenance.
Super K chose to "illustrate" Moses 2:28 with a hand-drawn black widow and a buffalo.
Now he gets out his scriptures and I hand him the pouch of colored pencils. I tell him what to read, then he lets loose with his imagination in deciding what to highlight. On the sixth day of creation, I might have drawn a stick figure to emphasize the creation of man--he skipped that minor detail, and chose to illustrate a couple of the animals he was proud to have "dominion" over.