Yes, you can use custom tilesets. Just remember that you need to specify how each tile should work. You can define them in the "Note" field in "Database" -> Tilesets" and in the bottom right corner. You have to do this for each tileset. As for having to create a new project, no, it shouldn't be necessary. However, if you have created your project in 2D, I do recommend creating new maps with the old ones as a blueprints considering that it doesn't translate well from 2D to 3D.