Mod settings across different saves

Mods cross over to all saves. If you want to create a save without mods, then start the game with mods disabled before you load the "unmodded" save game file.

There's no universal answer to this. It depends on the mod. Some mods apply their settings throughout the entire game and others apply them to saves. I would imagine that most of them do the former, though.

MCCC has a companion tool called MC Profiler that allows you to save different settings files. It overwrites the setting file via a launcher when you load from this program.

It just means you have to decide what save to play before launching and restarting the game if you want to switch save games.