Try to stick to the philosophy of "touch it only once". In other words, don't dump todo items or notes from one folder in OF to a temporary storage with the thought ... "oh, I'll just put it here until I know otherwise where I really want to put it ...". Rather, first decide what you want to design for your organizational scheme, then put the scattered pieces where they should belong in that scheme.
You could start with a blank OF database, design it as you want, and copy the desired tasks to it. This would be an alternative to shuffling things around. Here is a thread about it ...
http://forums.omnigroup.com/showthread.php?t=16803
In the meantime, you might also consider apps such as Notebook (Circus Ponies), Curio (Zengobi), or one of the other OmniXXX apps to store your document notes. That would get them out of OF because (as you noted) it is not the best storage option for them.
HTH
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JJW