I take it you've gotten TuneECU to hook up to the ECU? I'm using version 2.5.5.1 on a laptop. You will be in Map Edit (upper right bar). When the download is completed, the ECU goes through its startup routine, where you hear the fuel pump and the gauge needles move. When this is done, turn off the ignition, turn it back on. Under the ECU tab next to Display, hit "reset adaptation". Wait about a minute then turn it off. It wouldn't hurt to do the 12 minute tune but this just adapts the idle. It will adapt anyway after you ride it for a while.
Hook it up to a fully charged battery or a Battery Tender when reading or downloading tunes.