Check out puts a flag in Windchill that a file has been downloaded for modification and no one else may modify the file while it is checked out. Well, they can, but their changes would be outdated after you do your check in.
Check in is the process of uploading your modified checked out files back to the common space on the Windchill server so others may see your changes. It also removes the flag so others may now check out the file for further changes.
