Each judge scores each vault (two scores on each vault). The judges take the scores from the better vault, and average their 2 scores together.
For example:
1st vault
Judge 1 - 8.850
Judge 2 - 9.050
Vault Score (averaged) 8.950
2nd vault -
Judge 1 - 9.000
Judge 2 - 9.150
Vaut Score (averaged) 9.075
In this example, the 2nd vault would be used as the score entered for that gymnast. If the 2nd vault isn't nearly as good as the first vault, I've seen judges just say to each other, "So, we are going with the first vault", agree and not even score the second one. Hope that makes sense!