Can't seem to locate an easy way to change an NPC in game. Have a modded insert companion, not really favoring his name. but hesa cool looking dwarf, to thug my way through my villanous merchant character.

Creation Kit is the only way currently. The "setactorfullname" command doesn't work currently, and probably never will until, maybe, the SKSE team manages to find a method to inject a message string straight into your game.

Now if I edit a mod, and generally, I have to create a new ESP or ESM (whichever it turns into as a save). Do I run both the mod I edited (loaded into the construction kit) and the original. or just the newly edited version?

If it's an esp, you can just edit and save, but if it's an esm, you'll need to make a new esp.