Why does iBooks recognize PDFs that iOS7 Acrobat Reader doesn't?

As with virtually every Apple software application, iBooks leaves a lot to be desired.  Is there a save as feature for the PDF files I've overlooked that will enable Reader to open PDFs.  I can't believe I'm the only one complaining about this.  The main reason I prefer Acrobat Reader is that iBooks ignores PDF bookmarks and makes going to particular page a nightmare.era
Alternatively, can anyone recommend a 3rd party PDF reader to meet my needs?@

PROBLEM SOLVED:
As Steve Werner indicated elsewhere, (with the apple device connected to your computer, click on the device button on the top right, choose the Apps tab, scroll down to the bottom, select Adobe Acrobat, then click on the 'Add' button below to upload PDFs into Acrobat.  (now that I recall, I tried to do this once with the 3rd party iExplorer once but I forget whether I was successful)
It appears PDFs uploaded this way only become associated with Acrobat Reader and not iBooks.
Many thanks Steve!!!!

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