I would recommend asking on the Wiki discussion forum, accessible as a link from the Main page:http://www.canonipf5000.wikispaces.com
I haven't done any printing from the tray yet, so can't help you, but perhaps there are some other folks there who can.
I'm active on the wiki, but feeling more and more at home here too ;-)
Can you give some more descriptions around what you're seeing?
I have noted, when using the tray (top paper feeder) with cit sheets that the centered option gives some strange results with the CS2 Plug-in - scaling sometimes, image cropping at others. Still haven't isolated exactly which settings together yield best results.
John suggested at least 1" margins in a discussion on the wiki, and so far scaling images to that and using the centered options has worked very nicely.