the most important is the flicker menu.
go into it and change the values for each colour (using arrow keys) until you don't see the colour flicker. Do this after about 30mins of using the projector.
if you now play a disc, the imAGE shgould be more stable and generally look slightly better. People use this for reducing vertical banding but I've never seen that on my proj anyway.
To tell you the truth, I have absolutley no idea what the other menus do (apart from the self explanatory self check one that is )