MCServer doesn't (yet) migrate player data from Vanilla, so you will either have to store all the players' items inside chests in the map, or make the players lose their inventory.
As for the settings.ini, there's a [Worlds] section that has a DefaultWorld value in it, that's the name of the folder where MCServer loads the default world from. All new players that haven't been to the server yet start in that world.
It is possible to add more worlds to the section by simply using additional World values; you will need a plugin though to allow the players to move from one world to another.
There's also a Nether / End portal linking, but I think someone more competent should explain how that works; perhaps even write a short tutorial to the (now almost defunct) wiki. Hint hint, cheesedummy
As for the settings.ini, there's a [Worlds] section that has a DefaultWorld value in it, that's the name of the folder where MCServer loads the default world from. All new players that haven't been to the server yet start in that world.
It is possible to add more worlds to the section by simply using additional World values; you will need a plugin though to allow the players to move from one world to another.
There's also a Nether / End portal linking, but I think someone more competent should explain how that works; perhaps even write a short tutorial to the (now almost defunct) wiki. Hint hint, cheesedummy