I'm a bit confused by the rules..... it simply states to "even up" when, for instance one team has 9 players and the other 10.
So, would you roll twice for that last player on the 9 man team? That's the only thing that seems to make sense.
You can handle this situation in any way that seems best to you. The order in which the rolls are made for each team doesn't matter. My suggestion would be to find a way that you like and stick with it.