After a little back and forth with JAMF support I was able to get the following instruction set and application for creating manifest files for JAMF Pre-stage Deployments. As always be careful with links, I went back and forth on whether or not to post this link, since it is not the clearest way to determine what you are really downloading. Although if you want to go the safe route there is enough info when you click the dropbox link (before you download) to help you get a link directly from JAMF.
Here is the workflow for creating a Custom Manifest for use with Packages in the Prestage :
appmanifestbinary to usr/local/bin on a macOS computer : https://www.dropbox.com/l/scl/AACf7rKHA2U4TykFdyRZO7hL8nDhQx4zp7w
appmanifest -url https://your_url/path/to/yourpackage.pkg /sytem_path/to/yourpackage.pkg > /system_path/to/yourpackage_manifest.plist
Upload the package as normal using Jamf Admin. Or, copy the file to the web server through any method and then add the package record manually in Jamf Pro
Enroll a Mac and observe how it reaches out to your web server and installs your package.
Manually creating this manifest file is the best way to avoid hitting a couple of known issues, and has been approved by engineering teams.