Question: I already had NPE installed before I upgraded to the new version 360 this morning. I noticed that the new 360 has NPE included in the program...Do I need to uninstall the pre existing NPE and is there a certain way I should do it so I don't damage anything in the new 360's NPE?
NPE isn't really designed to be an on-demand scanning tool like MBAM. It should, IMHO, only be used if you suspect you have an infection and other tools aren't detecting it.
It has been known to remove critical Windows files with a result of Windows no longer starting, so use it wisely.