When I process files, NEO always puts the new Cineform file right next to the file it rendered no matter where I tell it to put them in the preferences. This is a pretty big pain when I have been shooting with the EX3 because you have to go through so MANY sub folders to import them into Premiere or if you just import the whole BVAP you have to go back and delete all the EX3 files. Is there a way??? What am I doing wrong???

Are you telling it to put them elsewhere? Inside the HDLink Preference panel, you can set the "Capture Location" and check "Use Capture Location for converted files."