If you have Acrobat Pro create a new Action (Tools - Action Wizard) and add your JS code as it's command.
Then run it on your files.
If you have Acrobat Standard (ie, not Pro) then you can't do it.
I have it in the action Wizard already... How do I run on all the files in the folder?
Select the folder under the Input part of the Action.
That doesn't seem to be an option, when i click on the button for it it just runs it without displaying any options first