Multi-file candidate applications are stored in the system as .ZIP archive files, a special kind of file that bundles multiple files into a single archive. When you want to update a multi-file application you will download the .ZIP archive, make the necessary changes, and then replace the original .ZIP file on the resume.
1. Download the existing .ZIP file
Read our article on how to download candidate files.
2. Update the .ZIP archive or create a new one
How you update or create the new .ZIP file will depend on your computer's operating system.
Windows users: To create a zip file, hold your Shift key and select the files you wish to include in the resume, and then right click on the list and choose Send To→ Compressed Zip file. More Information on .Zip files: http://support.microsoft.com/kb/306531
Mac users: Select the files in Finder. Click on the File menu and select "Create an archive..." or "Compress." More information can be found here: http://www.macinstruct.com/node/159
3. Replace the original application file with the new Zip file
Read our article on replacing a file in a candidate's application.