We attached plain skirting to our pantry doors with a fixing gun. You can also use Gorilla Glue. After the skirting was attached, we filled the holes with No More Gaps, sanded and then painted in Vivid White. We also filled where the previous handles used to be so we could change the handles and hinges to a stylish black.
There are no rules, but with wainscoting or panelling people usually put the bigger rectangle on top. We wanted to modernise ours so we used plain square skirting and made up our own design.