No, you don't do it game by game. You can't mathematically calculate ERA's that way.
ERA is defined as the average number of earned runs per inning (Earned runs divided by number of innings), times the number of innings in a standard length game. Thus a pitcher who gives up a run per inning will have an ERA of 7.00 in high school, but 9.00 in college or pros.
You have to ask someone in authority what the standard game length is considered for your league.
Around here, Legion games were 7 innings all season and 9 in the playoffs. I don't know what they would tell you, but since we're dealing predominantly with high schoolers, I would use 7 innings until someone told me different. Your pitchers will appreciate the lower numbers, anyway.
Another option is to list both ERA's, under stat columns labelled "ERA(7)" and "ERA(9)". That should make all the stat officionados happy.