At one point I could import files into an “import files” folder located in the Program files/Endnote X3 folder. Now that folder is not longer there and I can’t add another one.
What operating system are you using? Those folders are restricted and usually hidden in Vista and Win7. They might be there, but you can not write to them.
You need to create user folders in user accessible areas of your drives, and not in the Program Folders.