I have a tutorial half typed up on how to create these kind of tiles... I will finish it and post it tomorrow sometime but I use Tiled with those type of tiles all the time...
If you want to create those kinds of tiles don't worry about trying to convert the square tiles into those, set your tile grid to something like this: 64x32 (WxH) keep the dimensions to the power of two and draw in your square (diamond)... Something like this: https://copy.com/opacpd2cehya
Download this and load it into Tiled and you will see that it Tiles perfectly under the isometric map.
If you want a higher quality image and you want to increase the resolution/dimensions just remember what I said above...
Use that as your starting point if you wish, I will be creating a full tutorial on it tomorrow well I will be finishing and publishing it anyway lol.
I hope that helps?