I did not use a cover letter, but I did use labels to make it easier (faster) to sort through pages. I wanted to minimize the number of passes through the documents and minimize the time spent on each page to determine if our application was complete.
I used 3"x3" sticky labels to "clip" the documents together for each applicant. Place at the top of the pages like a paper clip with the sticky part on the side so it sticks to the first and last page. On each label, I wrote the applicant's name and "Adult" or "Minor". I suppose you could use real paper clips, but I don't usually stock those. I always have the sticky labels (light weight and don't add bulk).
For each applicant, the order of the documents followed the order in the checklist (except for the photos). They probably use the same checklist, so why change the order?
On some pages, I just wrote in blue ink at the top of the page what it was if it wasn't a standard document (for language evidence, but not for COPR) or if multiple items were on the same page (current and expired passports).
For 2 kids, we sent records for 5 academic years to cover 4 years of residency. That was over 80 pages of school records since each adult application had a copy. I used the sticky labels to "clip" the pages by child and year. Labels were "Education Records - Child Name" or "Child Name - 2011-2012".
Using this method, I added no additional pages.
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