1. Sounds like it's a mod installation issue. Is your armor mod a stand-alone version or a replacer? The former is usually a new set of armor that comes with an esp while the later just has meshes and sometimes textures. Also, when you removed the armor mod, did you also remove CBBE's body replacer? If you're playing a female, just run around in your birthday suit. if you don't crash, then we can probably rule out an issue with CBBE. If you do crash, then you'll need to reinstall CBBE and tell NMM to overwrite everything. The "underwear" that comes with CBBE is painted into the texture and is not a separate piece like the underwear in Schlongs of Skyrim is. If you're using the non-nude version of CBBE, tell NMM to uninstall and reinstall it, choosing the non-nude/sfw version again.
For #2, you'll need to learn how to set up armor for your body part in the CK (e.g. head, torso, hands, etc.), add the armor to the CK, add the ground meshes, position the armor properly on any body replacer (Bodyslide can help you do this for female armor), and how to use Blender. If you're just changing armor parts, then Blender is what you'll need to modify the armor meshes themselves. Others here have a lot of experience in making armor so I'll let them tell you what the process is.