Sorting iBooks PDFs and eBooks I purchased an iPad mini 2 not too long ago with the intention of using it as an eReader for the various PDFs that I own.  After uploading content to my iPad I tried to sort the content into different collections to help sort PDFs into different categories.  It turns out that moving PDFs into a collection does not remove the PDF from the original collection.  This is making it difficult to sort as not only do you have to search though ones you have already sorted, you have to remember which you've already sorted.  Is there a way to "hide" or remove PDFs from this main collection once they belong to another collection?  If not, is there another decent eReader app available for the iPad, or should I simply return it and find another eReader entirely?

**(Side note) It would be incredibly helpful if I could simply retain the folder structure that they are currently in, as they are already sorted and categorized on my computer.
For handling (a lot of) PDFs, I've found GoodReader to be the much better choice than iBooks. It provides a hierarchical way of managing content (similar to a filesystem) and also allows syncing/copying of whatever structure you already have on your Mac.