I just used a padded envelop that I purchased at the UPS store. And I did not include a return envelope and they do have their own. Padded envelopes are recommended instead of cardboard envelopes as they will protect your valuable documents more effectively.
I had two stacks of documents. Originals and copies. Do not have anything stapled or paperclipped as it is a hassle for your ECO to deal with.
I organized them in a way that made sense to me. From the top: biometrics appointment letter, receipts for Priority, applications, personal letters, financial information, tenancy information, and then lastly communication, wedding details and photographs.
In a small zip lock baggie I put my passport and passport photos.
I used one alligator clip on each pile to keep them separate.
It doesn't need to be more complicated than that. The ECO will put them in the order that they want anyway but it helps to have like documents together.