Various directions tell you when using a battery charger to re-charge a battery to hook up the positive clamp from the charger to the postive post and then to hook the negative clamp to a place on the frame vice using the negative post of the battery. Why is this?

so that you dont have a spark near the battery to help prevent a possible explosion. But if you hook it up before plugging it in then that should be fine.

Lead/acid batteries can emit hydrogen gas which can be quite explosive (think Hindenberg as a spectacular example). Thus avoiding sparks nearby is a cheap easy safety precaution.

Rods method is very good, or you could attach the pos.+ lead first and then the neg.- to prevent a spark. If you hook up the neg. first you will get a spark when hooking up the pos.

Well you can get a spark either way. Its just that if you hook up the pos first the spark will jump from the battery to the clamp, where as i you hook it up negative first the spark will jump from he clamp to the battery (using the electron theory of how electricity works) I would just hoo it up however you do, and then plug it in. This also puts you away from the battery a bit just incase something were to go wrong.