Alright, the title was the best summarization I could think of.
I go into the map editor, put together a map, save it in my custom story folder under my custom stories name and then a maps folder, but when I go into my 'c' drive (outside of the level editor), my custom maps do not appear. My maps folder remains empty.
However when I enter the level editor and then go to my custom story folder under maps, they are still there. For some reason I can't interact with them outside of the level editor.
A friend of mine walked me through a few things, including giving my user administrator privileges and full access to my computer's programs and revealing any hidden files in the folder options of the tools menu, but neither yielded any change.
I can access the .map files only when I use the level editor, and only to make changes to them. Obviously this means I cannot relocate them or access them in the game (as far as I know), and makes it impossible for me to make much more progress in my custom story.
Edit: An interesting point: When I ran Level Editor as an administrator, none of my custom maps appeared, where running normally I would be able to both locate and open them. My problem of course is unresolved, I just thought this was a curiosity.