Do they each have an individual Mii?
If they did, then it would be easy to track their high scores.
Beyond that, you'll just want to get or create a Tournament Bracket.
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You probably should have some sort of initial bowl off. If everyone has a Mii, then you can say something like the top 32 players will be in the tournament. Then randomly assign them to spots on the bracket. Or group them in 4's based on 25% levels.
1st position - top 25%
2nd position - 2nd 25%
3rd position - 3rd 25%
4th position - bottom 25%
Then have 4 people bowl against each other. Have them bowl 3 games each. Take the average of all three games.
Figure out the handicap and determine the winner.
Group up the next 4 winners and have them bowl three games again.
Repeat until you only have 2 left and have them bowl 1 game for the championship.