Saving as Package vs. as two separate files: advantages or disadvantages?

Are there any known disadvantages to saving Endnote files as a package? I have been using the two file system till now (X3, Mac).

Also, I note that my .enl file is typically empty (zero KB) whenever I generate it from an enlx file, so it seems to be doing very little real ‘work’. Which is why I ask. 

Thanks