Packages are saved programs that have resources saved inside them as well, such as GRP, SPU, SCU, BGU, etc. Packages are saved by using the following line:
SAVE "PRG:NAME","<package string>"
The package string is a hexadecimal representation of 44 bits, each bit represents a certain resource file. This is really annoying to do in your head, so you can just use this program: http://www.gamefaqs.com/boards/663843-petit-computer/69602216
Download the QR code and run the program, then use the touch screen to select the resources you want. Use the arrow keys to scroll through the list. After you've picked them all, write down the string on the top screen and use it when you save the program!
For example, I want to save my game with BGU0 and SCU0. I select them both in PKASSIST and it shows the following string: "10100". Then I quit PKASSIST (press select), load my game and the resources I want, and then I enter this:
SAVE "PRG:GAME","10100"
After this, every time I load my game, it will have the SCU and BGU files loaded inside it!