What you can do is modify the map with IGE, then save your game as a scenario (through the regular save game window, as I previously explained : exit IGE, open game menu, save, look for the checkbox to save as a scenario). The created scenario will retain the map and, I think, the civilizations, units, objectives, rules, techs advancements, etc. And you can then play that scenario or modify it in the world builder application. You do not need IGE to play that scenario, just as you don't need IGE to play a game previously modified by IGE (IGE is not tied to your savegames).
However, civ5 does not expose any feature for mods to change scenarios' settings. So there is no specific options for scenarios in IGE and there cannot be any one. The only connexion between IGE and scenarios is that any regular game can be saved as a scenario ; this is a standard civ5 feature, not an IGE one. And the fact that you don't need IGE to load a game or scenario modified by IGE.
Hope I've been clear enough and answered your questions. From what I understood, you should be able to achieve what you want to do.
However, civ5 does not expose any feature for mods to change scenarios' settings. So there is no specific options for scenarios in IGE and there cannot be any one. The only connexion between IGE and scenarios is that any regular game can be saved as a scenario ; this is a standard civ5 feature, not an IGE one. And the fact that you don't need IGE to load a game or scenario modified by IGE.
Hope I've been clear enough and answered your questions. From what I understood, you should be able to achieve what you want to do.
