Pencil you in on/for Sunday evening?

"For" is more natural to my ear.

Also "on" would be potentially ambiguous, as it might have the meaning "When it gets to Saturday, I will pencil you in". Not a very likely reading, I admit, but there may be cases where the ambiguity is more likely.

The choice of preposition makes little difference. I would use "for", but "on" would also be technically correct.

The real meat of the sentence comes from the phrase "pencil you in" which refers to writing an engagement down on some kind of calendar or schedule, but doing so in pencil rather than pen which is less permanent and can be changed if the circumstances change.