If you want different mod configurations for different maps, then you'll need multiple installs of the dedicated server - the server package for each map being in its own folder with its own launch script, rather than a single install with multiple launch scripts - or only use one map at a time and manually change the mod configuration between launches. In this case, you would have one copy for the modded server and one for the vanilla (assuming you want them both to be available at any given time). As long as you specify different port numbers for each, then you'll have no problem running them both at the same time.

Obviously you won't be able to share the same world file between each without a severe risk of breaking your world.