I upgraded my Edge to a Gryphon and did not get the cd but my guess would be that the cd contains the program Pegasus, which is needed to obtain custom tunes and update the Gryphon. Pegasus can be downloaded online, which is what I did. Changing the display colors, etc. and engine parameters are done throught the Gryphon itself using one of the options from the "main menu". To remove the Gryphon, you should put the truck back to stock just like you said. I would not remove the unit to prevent theft because each time you remove it from your truck, your truck should be in stock to do so and changing back and forth that many times I would imagine can't be good for your PCM.
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