The batch files are really just for the universe/league setups. So if you are playing in 3 multiplayer leagues that all use NFL teams, you wouldn't need separate batch files to load up each league.
I'm prett ysure you just "enter new multiplayer career" once the batch file for that universe is loaded up. Same league files and such.
I don't know how there wouldn't be some kind of conflict of interest with 2 teams in one league but I guess an owner interested in it could make it work.
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