I thought the same thing when I was sending in my application. Here's what I did and I hope it helps even a little.
1. Print out the Checklist for your region. The checklist should be numbered.
2. Organize all the forms and documents according to the order they appear on the checklist.
3. A lot of the forms say "if you have any other evidence attach it on a separate piece of paper" or something like that.
So I did, and I attached the "evidence" to each corresponding form. For example, for the question "have you ever visited your sponsor during your relationship" I attached photocopies of my passport page that had the entry dates to Canada on the form with the question. I also wrote in what each stamp meant.
4. So far you should have the basic application forms + extra pages you want to add following each form.
5. For the "any other evidence" part that supposed to prove our relationship is genuine, I put everything in chronological order, regardless of whether it was an email, photo, card, or letter. I also wrote in dates and details for everything, especially the photos. Example: December, 2009, Christmas party at in-laws. Left to right: mum-in-law, auntie whoever, uncle whoever, cousin, niece. Basically made a storybook of our relationship.
6. Finally, I used plastic 3M tab markers to mark each "section" of my application according to the things listed on the checklist. I also numbered the tabs according to the number on the checklist.
7. Then I went through the whole application three times JUST IN CASE I was missing something.
Giant pain, but it must have worked (or at least my plan of being a neatfreak didn't backfire) cuz I got a letter about four months after my husband was approved to be a sponsor
Best of luck!!