Yes, you have to set the id/index. I don't think you can change the id from the editor, so you would have to define your regions in the correct order, or hack the tileset's tres file.
To see the order you can click the "i" button or hold the "alt" key. The first number on the tile is the id/index, the second is the name.
For example in the tutorial's tileset the "+" tile is index 0, the "T" is 1, etc. So you would have to define your "+" tile first, then your "T". It doesn't matter where on you sprite sheet it is, or how it's named... it's the order of creation that matters.
You may just be able to move your regions around to put the correct id on the correct tile.
