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Yes. You will marry the AP to your ECU, flash the map you want and unplug. If you are getting an APV2 you can leave it plug in to use the new features.
A Protune will get the max out of your car, but there down sides. The biggest is most tuners don't back up your map. If you lose your map, not likely, you have to pay for another. Any parts added after the tune will require and touch up to your map. I would wait for a Protune until you get the car where you want it.
PS I have been run the AP for years and I added the Street Tuner software for my custome tuning needs.
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