What's in folders and what's not?

I recently updated to 5.1.1 from 4 something. It made a mess of my apps and folders. On the left is a list of apps with checkboxes to check whether or not to put it on the iPhone and on the right is a display of all the homepages and where folders and apps are located on them. As I move apps into folders they go into them. But looking at the list on the left I can't tell which apps have been put into folders or not. Or is there a way to tell?

I always just did it on my phone and transferred purchases. I always make purchases on my phone and transfer purchases to my Mac. Never kept the apps organized on the Mac. I always figured that since the connection between iTunes and iPhone is one way that if I organized the iPhone and the sync'd with the disorganized iTunes that it would disorganize my iPhone.

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