I used this guide to root my note 3, it worked flawlessly. Just be sure to install a recovery if you are going to flash or restore roms, etc.
I disabled Knox and it updates my prl without a problem. Knox is a security service used by businesses and such, so most won't actually use it.
If by the micro sdcard you mean installing apps in external memory and such, saw on the forums that the app "Folder Mount" solves this problem.