I’m using some tile sets I got from itch.io, the problem is there is one tileset for most of the land (grass, dirt, paths, etc) and another tileset for water (which includes grass on the edges). The problem is I can’t set up a terrain brush for the water because the grass is in a different tileset. Is there a way to do this or do I need to combine the two tilesets into one?
Indeed this is a missing feature. Since terrains are compared using their indexes, which are only unique within a single tileset, the algorithm currently can’t handle terrains from different tilesets. This is not unsolvable, but until it is solved, you’ll need to combine those tiles into one tileset.
Why is the water separate? Is it animated?