I've added some NPC mods to the game, however they are naked by defaut. How do I open them up in the creation kit to edit them? Is this possible?

Load the mod in the CK and find the NPC in question. You can give them a generic outfit (there are many to choose from) or you can create your own outfit for them and then assign the NPC to wear it.

I'd also suggest taking a look at the http://www.creationkit.com/ in general, lots of useful information, and specificaly this page to get started: http://www.creationkit.com/Video_Tutorials!

The thing is, how do I load the mod? What menus? I've used UnrealED years ago but this isn't the same

You open the Creation Kit and click File | Data and chose the ESP (mod) you want to load.

I really suggest you take a look at those videos. This is covered in the basics.

I've tried that before, says multiple master files selected, even though I didn't pick any, load aborted.

Maybe someone else can answer because I haven't seen that error. I load my mod with both Skyrim.ESM and Update.ESM without a problem.