If there is a large voltage difference between batteries you will get a spark as the current tries to flow. If you have one flat battery and one good battery as soon as you connect large quantities of current will flow from the good to the low battery.
As long as it only sparks as soon as you connect the leads and the leads do not get warm you should be ok.
I assume you mean you have connected the positive and then when you connect the negative you get sparks.... If so this would be normal as current will flow from the charged battery to the dead battery and the Ignition circuit etc if switched on...
Only if you're attaching the leads to an ignition switched one.
Usually battery to battery so ignition position is immaterial. Even on the bikes with jump posts etc I can't see you jumping to an ignition switched lead.
Make sure that the contacts are clean.
I was wiring in a cig lighter extn lead to my battery a while back and as I screwed on the 2nd contact I could hear a crinkling noise and a smell. It was the wire getting very hot and contracting the plastic covering of the wire. Turns out that the ends of the wires had a bit of grease on them. Cut it off and new wire showing did the trick.
Only if you're attaching the leads to an ignition switched one.
Usually battery to battery so ignition position is immaterial. Even on the bikes with jump posts etc I can't see you jumping to an ignition switched lead.