I’m trying to set up Tiled to make level design easier for a 2d platformer. The problem is, all of the autotile tutorials I’ve found are for different types of games. Following these guides would make my terrain look like this:
And when put to use, this terrain comes out like this: 
The problem is, it seems to be drawing where the tiles aren’t, so when you click, the tile clicked upon is surrounded by wall tiles. How could I set this up in a way that makes it easier to use?
I think you just need to set up your terrain in reverse, since the white parts are nothing but a transition from blue to transparent/nothingness. So, blue = terrain, white = nothing, and then you should be able to draw the terrains as you want them, if I understand your tiles correctly. If I misunderstood, could you please provide an example of how the tiles should be arranged?
This is how the terrain tool is supposed to work. Its effect is limited to selected tiles, though. So you can use the Rectangle Select tool to create a mask.