1. Your image needs to be 24-bit. To do this, go to Colors --> Increase Color Depth --> 16 Million Colors (24-bit). Note that JCS cna onlty take tilesets that are 256 colours big, and by increasing your colour depth to 24-bit you would have to do a load of other things to convert it back to 256 colours, mostly involving palette editing. Also, this will reduce the quality of your tileset by a LOT (You try and put 16 million colours into 256 colours).
Explaining all of that is a whole different story, and could fill in an entire huge tutorial all by itself, one I'm not in the mood fo explaining right now

2. What sorta ground tiles are you talking about?

3. You guys ever played MDK2? I finished it ages ago, but man! I seriously have the urge to play it like never before, too bad I LOST THE GAME!!! WAAAHHHH!!!! *dies*
That was the only third person shooter I'd ever dare to play, JK2 sucks.