Look into the Notebook apps - they are perfect for this type of thing as they let you group logical ideas together much like a true paper notebook, rather than keeping track of a bunch of individual files. Ones to consider might be Evernote (great cross-platform support), Notebooks for iPad (seems to be good if your primary focus is typing and maybe inserting a few documents), and Underscore Notify (best overall concept but still a little buggy. Type, draw, write, insert documents, pictures, web clippings, etc. And mark them up in a very flexible manner.)
One thing to consider with some of these apps though is that they don't always have a way to back up the files directly - you can email or export copies of your notes, and everything is backed up to iTunes, but with some of them, if you set up a new device and don't want to or cant restore from a backup, there may be no way to restore your notebook to the working order it was in.