I'm not implying you are doing anything wrong, it is just difficult to talk about knot tying via written text. Here are a bunch of random facts that I hope answer your question:
Usually when tying knots, using the needle driver or your hands, the needle is either:
1.) taken off the suture while tying by hand
2.) laying somewhere in the sterile field away from your hands, since the suture should be long enough to avoid the needle
You should not be holding the needle in the palm of your hand while tying. Also the suture should not be so short that you are having to grab the suture around the needle. If your suture does get this short, grab another one.
Hope this helps!