I wouldn't worry about it all too much. Just use your best judgement. I sent back secondary's that were 3 pages or less in a small envelope, folded three times. Secondaries that were 4 or greater I got a large envelope. Folding won't get you into any trouble, as I've gotten interviews at places I sent folded applications to. As far as letters of rec, I don't see that you have much of a say in that, as whoever is sending them out will do whatever is most convenient for them.
As much as we believe that every little thing we do is going to affect our ultimate outcome, I can't believe that adcoms look at things like how crooked we put the stamp on the letter or how neat our handwriting is on the application fee check. Spend time worrying about the more important things, like kissing the adcom's butt on the "Why do you want to go to X school" essay
🙂