So I just hit 100. What's the deal with the elite skull guys. Am I supposed to be hunting them? (I guess my mod colors them as blue skulls?)
I think you're using Rarefinder?
White Skulls: Unique Rares. Higher HP than normal for a mob of their level. Usually drops Rare gear, or flavor stuff like Toys and consummables. Can also drop Garrison Resources (!!!). Can only kill each once per character.
Blue Skulls: Mission Rares. From your Garrison, you'll get daily missions that reward a bucketload of Apexis Crystals. The PvE group ones are typically called "Assault on X", where X is one of the 100 mob zones around Draenor. The Rares in these zones have massive HP, usually give Apexis Crystals/Primal Spirits/Gear, and count heavily towards quest completion. They're meant to be done in a group but not all of them are elite and many can be solo'd if you burn cooldowns and your class is naturally tanky/healy.
Red Skulls: Repeatable Rares. I'm not sure what their loot tables are like to be honest. I haven't really tried hunting them yet.
EDIT: Shit, I need to get in on this scribe stuff.
How much skill level do I need to craft the recipes, if any? I'd just focus on the high demand glyphs.