level.dat is not used by MCServer at all. It is only written, if it's missing, so that tools such as Minutor work correctly on MCServer-generated worlds.
MCServer uses the spawn position specified in world.ini. Also, if a player has already been on a server, the player's position (naturally) supersedes the default spawn position.
As for SkyBlock, it's a rather old map, are you sure you have an Anvil version (.mca files) and not the older McRegion version (.mcr)? The easiest way is to let MCServer generate a world, then delete all its .mca files and replace them with the .mca files from the imported world. That should always work. Just make sure world.ini's storage schema is set to Anvil.
MCServer uses the spawn position specified in world.ini. Also, if a player has already been on a server, the player's position (naturally) supersedes the default spawn position.
As for SkyBlock, it's a rather old map, are you sure you have an Anvil version (.mca files) and not the older McRegion version (.mcr)? The easiest way is to let MCServer generate a world, then delete all its .mca files and replace them with the .mca files from the imported world. That should always work. Just make sure world.ini's storage schema is set to Anvil.