Is there a way to align the directional lighting in the map with the sun in the .sky file? Do I have to eyeball it? Use trigonometry? Copy and Paste?

Set the sun's position first, look at where it is in-game, and then set the directional light.

so eyeballing it is then.. I was just hoping for a more accurate way..

A more accurate way would be to set the sun's position and then go in-game. Find where the sun is, and make sure your unit is directly facing the sun. Then rotate your unit 180 degrees such that your unit's backside is parallel to the sun. Bring up the minimap display, and take a screenshot for reference. You now know in which direction your directional lighting has to point in relation to North based on your unit's arrow.