You can include all of the files, just to make sure you have them, but you only need to include the ones you actually reference.
While in development, you typically use the standard files, then when you're ready to publish, you switch to the .min versions to save on load times.
When I update the files to the new js files, I get weird formatting results. Any thoughts?
You should probably start a new thread with the new problem.
If you can post a link to a page where the problem occurs, that would be best.
Make sure to describe what is happening vs what is supposed to happen and I'm pretty sure we can get you straightened out.
Did you decompress the folder contents first with WinZip, StuffIt or 7-Zip? If you don't the files will not be usable.
See Primer for using jQuery Plugins