To set up an isometric tilemap, create the tilemap and start painting a few tiles into it.
Then, in Settings
Tile Properties
change Tile Type -> Isometric.
You'll now see the tiles offset correctly for isometric.
Now tk2d needs to be told how big the isometric tiles are.
Reduce the vertical size so it now aligns correctly.
After that, change sort method so they're all drawn in the correct order.