Title basically says it. How do you go about packaging your entire .esp together, including all the custom scripts? A buddy just tried to send me his mod, including his Scripts folder, and none of them were attached to where they should be in the CK. Is there a way to have the scripts come attached to everything when you distribute your .esp?

What you described above should work. It's how loosely packaged mods operate. When people talk about a "loose files" version they are referring to mod assets that aren't packed inside of a .bsa archive. He or you must have gotten the paths wrong at some point for this to not work.

If he want's to include everything in a .bsa archive, the Creation Kit has built-in support for that. http://www.creationkit.com/File_Menu#Create_Archive. The article also recommends http://creationkitadventures.wordpress.com/2012/02/25/how-to-package-a-bsa-archive-for-skyrim/, which seems to provide a more in-depth explanation.