Hello, I'm having major issues with using any custom-made scenes.

Basically, when I use the scene editor in-game to create a map for myself (let's say a bunker map for a defense game), it runs fine for the amount of time I have the game open. However, if I then close the game and try to open it another time, any custom scenes I have made cause the loading to fail, with an error message saying the scene can't be loaded.

What do I have to do to be able to use these scenes?

That happens to me too.
Apperantly, It makes a Scene.ini
It goes to Modname.rte/Scene/Whateveryounamedyourcustomscene.ini
I don't know why it doesn't make the folder and ini

So what does this scene ini have to do with the problem?

it's the scene.ini of your costom scene.
that's what.

I understand that, but knowing that there is an ini isn't answering my question. I need to know why the game fails to load any level I make after I close the program and re-open it.

because somehow your editor is defective, and is saving your mods incorectly; thus causing an error.