Well, the simple answer is, if every thing is working correctly, turn all of them. They will only turn 90 degrees, or 1/4 turn. The long answer is, you want to stop the flow of water in to the water heater, so the bottom one is inlet, make sure the handle is crossways to the the plumbing. You don't want to back feed the outlet of the water heater, so make sure the one is closed, crossways to the plumbing. You do want to bypass the water heater, so make sure the one feeding the bottom line and the top line is open, in line with the plumbing.
Hope this is the answer you were looking for
2012 Ford F250 ext. Cab 4x4
2002 Jeep Wrangler Sahara
2008 Yamaha V-Star 650 Classic
2008 Work and Play 18LT