What do I do when I have an empty row/column when making a Karnaugh map?
You need to give a better idea of how you've laid out your map, but I'm guessing that your "empty column" represents the two states (out of the eight total) that you're not using.

While you could use them as "don't care" states to potentially simplify the final logic, it is generally better practice to add those states to your state diagram, and make sure that they lead back into a legal state, in case the logic somehow gets into one of those states (cosmic rays, power-up, etc.)