I'm just lost. For instance, how would I store separate maps? Do I just write them to and read them from a text file? Or...?
You can store them in a custom binary format, or some custom text format that you create (as you suggested). There are many possibilities.
And drawing things to the screen... considering isometric display with heights and bridges/overhangs and characters walking and having to jump to different heights and all that... AND making it look smooth... ugh.
I would begin with the map editor. Get the terrain rendering and don't worry about characters or anything until later.
Is this going to be isometric sprites. or 3d rendered in isometric view? Is there a game with the same isometric style you want? Any more detailed information would help us help you.