Using my IPad Mini 4, I put the owners manuals, etc in IBooks and put the IBooks icon next to the IFly GPS icon. If I need to refer to something, I click the home botton on the IPad, then the IBooks icon and there it is. I have the POH for the SkyCatcher and Remos I fly, as well as manuals for all the different avionics on both airplanes. If you know you're going to need it, you can open the document in advance and go to the page you need and it will be there when you click IBooks.
Sometimes, it's better to use other apps rather encumber one app with too many functions.