It depends on the mods. Many add their own features to world generation, such as new ores or trees, and have to be enabled in your world prior to world generation. Others add new recipes or other functionality which does not depend on new worldgen features, so you can enable them after worldgen.

Once mods are installed, you can enable and disable them on a world-by-world basis using the Mod menu when selecting a world under New Game. All mods are disabled by default, so don't forget to enable the ones you want after creating a world and before playing in it for the first time – it is entering the world that actually starts up the world generation!

Hope this is helpful!