The main way to get them is through doing writs. These can be collected from any main city in your faction zones.

The maps you refer to are surveys. They are rewards you sometimes get from completing writs. You'll often get rubbish (a sword or bow etc). You'll get trait gems and even legendary improvement items. The higher your blacksmithing/woodworking/clothing the higher the chance of getting tempers. It has to be rank 9 in the skill line to deliver it to craglorn. This is how you

The surveys will lead you to about 7 or 8 nodes. As well as wood or metal, you'll have and increased chance to get nirncrux compared to standard nodes. These nodes are only there for you and only appear once you open the survey (like a treasure map).

You can get nirncrux from standard nodes, but at a far frequent rate. I've done about 40 writs at top level and got 3 reinforced nirncrux and 2 potent nirncrux.

The craglan main questline is nothing to do with nirncrux. However, when you complete it, you'll get rewarded one random Nirnhoned item. It could be anything. So you can then research it and use nirncrux to create that item after research it's done in whatever style, material and set you like.