I am not aware of any means of scripting a checkin or checkout action with Excel Macros. If you can identify the updated files on your local hard drive, you can just drag-n-drop them to a Windows Explorer window open to your Windchill server with Desktop Integration.
You don't need to drop each file into their "home" folder in Windchill. Drop them on any folder in Windchill and they will auto-resolve where they need to be checked in to.
The only caveat to this process is that you cannot mix existing files ready for checkin with new files that do not exist in Windchill. You will need to drag-n-drop the group of new files first and then drag-n-drop the checkin files next.
Windchill 10.2 offers a capability to identify which files have been in Windchill using Desktop Integration. Check out all the new features with the presentation linked to What's New in Windchill 10.2 M010-M030 for Document Management.