You hook the SCT up to your laptop with a USB printer cable and log with the LiveLink software from the sct website. Bama can send you instructions on how to do a datalog and send it to them for review. They have been really good about reviewing them and sending tweaks in the past, and I definitely recommend doing this.
Another tip, make sure you relearn the idle and fuel trim strategies. This needs done any time you flash a tune, disconnect the battery, or the battery loses charge. The procedure can be found in your owners manual bit is pretty easy. Put the car in park (or neutral with a manual) and set the parking brake. Turn off all accessories (radio, ac, etc) and start the car. Idle it until it reached max operating temp then let it idle for one more minute. After that, turn the ac on and let it idle for at least one more minute. To complete the process you need to drive the car at least ten miles before shutting it off.
And I have never seen it running too lean, but bama did adjust one of my earlier tunes based off a datalog that I sent them since they thought it was a tad too lean at some points.
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