I would advise against submitting your application in binders, or any other similar thing. the IOs will just remove your documents and thrwo out the binders. They separate the application into different parts, anyways.
just paperclips, binder clips (for groups of paper larger than what a paperclip can handle) and rubber bands should be fine.
I too separated my application into 3 sections: 1) sponsorship application 2) immigration application and 3) proof of relationship.
I ordered all of my supporting evidence for the first two sections as outlined in the document checklists. Then I made a table of contents for the proof of relationship section, detailing all the evidence that could be found in that section (i.e. proof of address, proof of joint accounts, cards and notes, photos etc). I clipped each section together with a large clip, and then put a rubber band around the entire package and sent it off.
If you search on this forum, you will be able to find threads with pictures of people's completed applications, but I don't remember the thread title, off-hand.