If you have an encrypted PKG from a retail disc or download, paste the 32-character key into the designated field. For fake/homebrew PKGs, leave it blank—the tool will auto-detect the null key.
If you are using a tool like PS4 PKG Tool, the process is incredibly simple:
Apollo is currently the gold standard for PS4 homebrew management. While it is known for save management, it has robust file management tools.