Hey Polomeo! Thank you :) I'm glad you like the assets.
Autotiling is a complicated thing and unfortunately there isn't a single way to implement autotiling for a given tileset.
I'm not a dev myself, but I try to provide the tilesets in Minifantasy in a way that can be adapted to most use scenarios. To achieve this, I'm always in touch with devs that often use the collection for their projects to ensure that the way in which tilesets are provided is flexible enough to fit a broad scope of different dev needs. That said, you will probably need to prepare the assets to meet your specific needs based on your game engine and project requirements.
If you are part of a dev community, asking other devs about how they implement autotiling in X game engine will probably get you good solutions (in Discord or Reddit, for example).
Alternatively, there are lots of tutorials on YouTube that will guide you step by step to get autotiling working in your engine.
For the ground tiles, setting up autotiling is easier (look for Wang Tiles system). However, for more complex sets, like cliffs or walls, you will probably need Rule-Based Systems. These are way more flexible but setting them up requires more work.
I know this is a long answer with no direct solutions, but I hope this, at least, can direct you towards some answers.
Good luck!