"Bearing in mind I will now have one hard drive (though probably partitioned if that matters) what should I do about the jumpers on the hard drive? I hope you understand what I mean."
If you will be only having one hard drive installed that would contain Windows etc, then this drive would need to be set as the Master (by use of the jumper plug). There is usually a diagram on the hard drive indicating where the jumper needs to be plugged to set it as master.
"With regard the IDE cable that comes off the mother board, it has 2 plugs on it, does it matter which plug I use?"
Have a look now before you remove any of the hard drives and see where the master drive is at now, also take note of which IDE cable is plugged into the master drive now before removing it then that way you can attach the new hard drive up with the same IDE cable has before. It may be useful to draw yourself a little diagram, I usually do this if it means I will need to remove wires or other items that may need to go back in the same spot.