Don't bury any stem that was originally above ground. There is a narrow part at the very base of the stem called the hypocotyl (the embryonic stem) which I would not bury either, but there's some wiggle room for that part if your soil is open and there's not a lot of top dressing above it. You definitely do not want soil touching the wide part of the stem, where the true leaves and spines start. I hope that's clear. Remove the soil to where you can clearly see the narrow part (and keep the soil level across the pot) and then top dress up to the base of the main stem, or lower.
