I know when a set bonus is active it shows in blue but I'm not getting the 8 piece bonus? I have the Karlstein outfit equipped with the weapon skins. I also have the undergarments equipped along with an accessory which makes a total of 9 slots taken up, shouldn't it be blue?

Accessories do not count as part of the set bonus so it shouldn't be possible to get the 8 piece bonus until awakenings come out and you can equip an awakening weapon skin.

I have 2 weapon skins. Do the others that come out take up two slots? Maybe I'm confused on how it works. My uhh undergarments take up slots as well.

Currently you will have a main and off hand weapon skin. Awakening is a different weapon slot that is not available yet.

So to get the full 8 piece bonus you need to fill head, armour, gloves, feet, main hand, off hand, awakening and underwear.