Between every two times you activate the script, you should exit EB. If you only save and continue the game, there's no need to restart EB.
It may be a small effort but... imo EB is a sufficiently long game (both in battles and campaign-play), so I don't really feel any need to play two different factions at the same time. How can you keep trace of all army movements, army compositions and the great construction strategy, let alone role-play, in two different games?
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