The secret to quick and efficient trimming in any plane, in real life or the sim, is to use the yoke or stick to set the desired attitude first, then use trim to hold it.
I may be wrong, but it sounds like you're "flying with trim", which although not impossible, can be a very sloppy way to do it.
It shouldn't take that long to trim for level flight unless you are adjusting pitch with trim... not sure about your problem with the AP, but it is possible that the AP will take drastic measures when it is engaged after you've overtrimmed the plane.
Always set neutral trim as soon as you level off (the wheel should be marked), then try to hold the plane level and add trim in very small increments- moving the trim slightly then releasing the yoke briefly to see what happens- until you can fly at the desired altitude hands-off.
This should be relatively easy in a large aircraft. .. I don't often fly big jets in FS9, but it usually only takes a few minutes at most for me to trim them... although I will often let the AP level off for me.
