Keith Jordan, one of the authors of the Santa Fe reefer book, responded to an e-mail on this subject:
The cars would originally have the reporting marks on the diagonally opposite hatch covers, then sometime in the mid-fifties they started putting the reporting marks in the middle of the roof as well. It does depend on class somewhat, as the roof-top reporting marks were first put on those cars where the hatch covers would lie flat and you couldn't see numbers on them.
The GATC-built cars of the mid-to-late thirties had reporting marks on all four hatch covers, not a standard practice. For Brian's RR-44, I'd put them on the opposite hatch covers.