Arranging apps on ipod touch not possible with itunes 9?

I spent some time at work today arranging the order of my apps on my ipod touch and got everything layed out how I liked. Then I came home tonight and synced my ipod with itunes 9 and all my apps have been re-arranged to match the order they are within iTunes. I assumed when you sync it would look to see which had the most recent changes, ipod or itunes and then sync in the right direction. If itunes always re arranges the order of the apps what's the point of being able to arrange them on the ipod if the changes are going to get lost next time you sync?
My other question is that i've deleted a few applications from my ipod but they don't get deleted from itunes. Therefore i'm always having to remember what i've deleted in the day so I can delete them from itunes as well. Is there anyway to get the ipod and itunes to sync so that they contain the same apps and therefore not having to delete apps twice?
Thanks

I rearranged my apps on my Touch and then synced it to iTunes to see what happened. When I ejected my Touch and checked my apps were still in the manner that I arranged them so the method you are having issues with works perfectly fine for me. Also, looking at the online manual about the syncing of apps it states:
+iTunes automatically syncs applications you’ve downloaded or purchased on iPod touch to your iTunes library when you connect iPod touch to your computer.+
+_This lets you access the downloads on your computer and provides a backup if you delete applications from iPod touch._+
Based on the underlined part it is my understanding that iTunes is not set up to delete the items from your library just because you deleted them from your Touch...it keeps the apps in the library as a backup until you delete it from iTunes so that's just the way it is. As for the apps arrangement issue...if you haven't already you may want to try reinstalling iTunes 9. Not sure if that would fix the issue or not though. And not sure if anyone else is having that issue since no one seems to be posting that they too have experienced the problem.

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