1. Go as high as your available light will let you and still keep exposure good. This will give you very crisp edges without any motion blur. If you take it to AE or use special slo mo software, it makes the math a bit easier.
2. Go twice as fast as you slow it down. meaning if you will slow it down to 60 fps, shoot at a shutter of 120. If you will slow it down to 1000 fps, shoot with a shutter of 1/2000. This will give you a more natural motion blur, replicating a high end high speed camera.