[Saber Cherry]

It only affects games you create while the mod is enabled, not games in progress. Their mod system works really well! You don't have to manually enable / disable mods after a game is started, it is all handled automatically. For example:

0) You are already playing 2 games, Game A and Game B, with no mods.
1) Enable Arralen's Ulm mod, "Black Steel of Ulm".
2) Design a pretender.
3) Start a new game as Ulm, Game C.
4) Load Game A - the "Black Steel of Ulm" mod will automatically be disabled.
5) Load Game C - the "Black Steel of Ulm" mod will automatically be enabled.

So you can play multiple games with mutiple different mods, without paying any attention at all or doing extra work.

Just be sure to have only the desired mods enabled when you create your pretender and when you start a new game, and everything else is automatic.