Lava levels: Create your level in a map editor - omen is the best, imo - then add it to your minecraft server folder and call it "server_level.dat".
Saving maps: When you turn a server off the map is not deleted, as long as you never replace server_level.dat in the minecraft server folder the level will stay the same. If you want to backup a map save server_level.dat to another place - copy / paste works fine - then when you want to restore move it back to the folder.
It is easy to misunderstand what is top and bottom in omen. I am ATM too tired to remember it, but I do know it is somewhat confusing. Play around with the map a little to learn how the coordinates work.