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We had a California OT, and I was able to start inning by placing a runner at 2b. No problem. But as OTs advances, umpire said we start with one out. I couldn’t find out how to start inning with one out and have a runner on 2b?

There is no way to add an out. However, after two outs, select, 'Misc | End Inning'. This is the normal procedure for handling this situation.