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How long should I leave it unhooked? And are you talking about starting it then turning it right back off twice before the third start?
Leave it disconnected for 5-10 minutes, just long enough to ensure all power is drained. It might be done in one minute, but why rush it. Don't forget to hold the key in the starting position for 30 seconds while the battery is disconnected.
Starting 3 times - Buckle up, start rig and let it go through its checks, then when all the dash lights go out shut it down. Wait a few seconds, then repeat. On the 3rd time, let it run for at least 5 minutes.