It took a while to find this information and I ultimately had to ask our JAMF Software Account Manager for it to help us troubleshoot some JDS issues.
I figured I would share this since the office JDS documentation doesn't give this specific work flow (at least none that I could find).
1.) The package is first uploaded to the master JSS Tomcat instance. 2.) After the file is completely uploaded to the tomcat instance it is uploaded into the database in the downloadable_file_chunk_data table. 3.) The downloadable_files table is where the root JDS looks to download new packages when it checks for policies. An entry in downloadable_files is made after the upload completes in step 3, indicating the package ID, name and that the package is ready for download. 4.) After the package is loaded to the database, the file in JSS/Tomcat/temp/ is removed. 5.) When the root JDS checks in for policies (every 5 minutes) it looks to downloadable_files and begins downloading. 6.) The file is downloaded to tmp where it is then copied to /JDS/shares/Caspershare/ after the download completes. 7.) The data should be flushed from the downloadable_file_chunk_data table after the upload to the JDS is complete. 8.) The package will appear under the Distribution tab of the JDS after submitting an inventory update which should be done automatically as part of the download process.
