I would suggest you 'start from the end." 
Create the PackageManifest.json first. (Call it anything, but PackageManifest is common.) It's the json that tells HPM what you define as the package. Might be one file, might be a hundred, split between driver code, app code, files and bundles. Put that file adjacent to your source code. That provides you the Location you will need for the next file: repository.json or repo.json. Anything you want to name it, but a variation of repo is common. This file is YOUR collection of Packages, pointing to the PackageManifest for each. Finally, with the Location of your repo.json in hand, create the change that you want added to the Master Manifest. It's two lines inside some json braces. The name you want and the location of the repo.json
There's a cute little package to assist with generating HPM json files:
HPM Manifest Generator or install it via HPM.
Also the developer section of HPM's documentation will send you to:
for another tool to create the json files.
