If it is one I have stored in OneDrive I either just make it available offline in the OneDrive App or use the Open in Another App feature to move it to iBooks. Same thing if I find a PDF online with Safari, I just use the open in another app feature to import it to my OneDrive or open it in iBooks.
I also use the Documents App by Readable to manage a lot of my files on my iPad. It is linked to my cloud accounts so I can access any files from it.