To set the spawn for an individual world using Multiverse, first make sure you have Multiverse Core installed.

Next, go to the world you want to set the spawn for using /mv tp <worldname>, or /mv tp <worldname> [--unsafe] if it will not let you teleport because it is "unsafe" (be prepared to switch gamemodes or use /fly if you do this). If you are unsure what the exact name of the world you want to go to is called, type /mv list to see the worlds you have available to teleport to.

Once you are in the correct world, move to the location you would like the spawn to be at and use /mv setspawn. This would need to be done for each multiverse world if you want to specify their spawn location.

If you recently installed Multiverse Core and are wanting to create a new world, please follow the guide here.