Normally the trick is to firstly make sure the holes end up in the right place, then screw the screws a bit the wrong way till you feel them slip past the start of the thread on the other half then go the right way, and normally this stops the cross threading. Do not do one up a lot before you get the second one in the same way. It is a tactile thing though, and if the holes are just a little bet out or too small, its a real pain.
I've done loads of these on doors and the only issue was actually making sure the things lined up.
I'm surprised nobody has made handles with those little rotating cams on them that they use on chipboard hinges by now! Brian