If you haven't already done so, I'd start by reviewing this thread:
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That should give you everything you need to understand how to use TuneECU.
Then, assuming you're installing the Jardines and the triple filters, the fourth post in this thread has a tune that should work for you.
As for installing the filters, this thread is the gold standard on doing the job:
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I believe you were having the dealer install the Jardines. If not, its a simply a matter of starting from the back and removing the stock system. Then work in reverse, following the instructions that come with the Jardines, install from the header back. Its an easy job shouldn't take you more than an hour or so.