Runner goes home during called 3rd out on another runner

[ksnow]

I'm sure this is a simple question, but I want to make sure I'm doing it right (so my stats don't look weird later, when I find out I've been doing it incorrectly). I was scoring a game last night, with a runner on 3rd and a batter up with 2 outs. The batter hit a line drive to right field, and was thrown out trying to get to second. In the meantime (and before the batter was called out), the runner on 3rd scored. I kept trying to start iScore with the batter, but couldn't figure out how to credit the runner with the score, so I went back, scored the runner on 3rd first ("advanced by batter"), then went back and scored the batter out. Is this correct?

Thanks in advance for help with this.

[Danger]

I would score it as IN PLAY>>SINGLE. Then I'd tap the runner on third and advance him home ADVANCED BY BATTER. Then I'd tap the batter who is now on first and mark him as out at 2nd base OUT>>TAGGED OUT 9-6.