as soon as the flight has been loaded the autopilot has to be reprogrammed from scratch - and in the meanwhile your airplane will just go crazy unless you get someone controlling it manually while you input data into the AP (or the other way round)
Puzzled over that for a while, FridayChild - I've had the 'A/P off' problem occasionally, but have never had any trouble holding the thing steady with the stick while I check the settings.
Then it dawned on me how lucky I am (in the FS9 context) to be left-handed - and also to have learned to fly long ago in aeroplanes with a central joystick and engine controls on the left.
Are you by any chance using the same hand for both stick and mouse? So you can only use one or the other at a given time? If so, you might consider switching either the mouse or the stick to the other side. Wouldn't that pretty well solve your problem?
As to which side, doesn't much matter, eventually you'll have to master both. Most modern aeroplanes have side-by-side seating with the captain's position on the left and the throttles etc. in the middle. But if you ever take up flying for real, you'll be the junior partner for quite a while, with your right hand on the yoke and your left working the throttles and making the settings; so that's probably the best arrangement to start with.
Now that I've written this I'm not sure whether to post it - maybe you (and everyone else) are already using both hands. But the silliest question is usually the one you don't ask - if you ARE trying to do it all with one hand, maybe this will help.