If you write something in pencil, lápiz, it can be erased or changed. If you write something with a pen, bolígrafo, pluma y tinta, it is permanent and can't be changed. To "pencil something in" is an idiom. It means to make a tentative plan, with the understanding that the plan might need to be changed. "Should we meet for a picnic lunch Saturday?" "I'm free. I'd like to. But the forecast says 'chance of rain.'" "Let's pencil it in for Saturday. I'll call you Saturday morning, and we can decide then."

It’s not about the pencil. It just means to add a meeting in a calendar/ date book. It’s still used in the electronic age to mean add to calendar even though there’s no paper/pencil.