As far as I recall, at least one of my son's MOC's didn't request that everything be sent in altogether, but we felt that surely this would be easier to avoid anything going "missing" in transit. (Remember to follow up that the MOC's office has received everything before the deadline).
When requesting the recommendation letters, son sent an email to the teachers/scout leader/others explaining his request (personalized and with all the relevant MOC names, addresses, and specific details) and his desire to attend the academy (mentioned that his visit to USNA last spring and the Summer Seminar experience helped confirm it), and attached a resume for their benefit. He explained that he would stop by with an addressed envelope that they should use for the letter, then seal it and sign across the seal - regardless of whether or not this was requested, we felt it was easier for the teachers etc. to do this for all the letters. He kept in contact with them and then stopped by to pick up all the letters (his school requires you to give the teachers 2 weeks for recommendation letters to be completed). Those that needed to be mailed separately (including his transcript to go to USNA), were ready to go and the others were added to the whole MOC application package, remaining in their sealed envelopes. It is also comforting to know that you are keeping control of everything and that the letters have actually been mailed.
The actual Naval Academy application doesn't ask for any hard copy letters, but as you are completing the online application, you are asked for your guidance counselor and 11th grade Math and English teachers' names and email addresses. Again, send them an email letting them know the request will be coming and include your resume. Some folks reported that you need to be sure to follow up that the teachers received the online request because sometimes it will go into the school's SPAM folder - son attends a huge public school and there were no problems at all.
A couple of the people gave him a copy of their letter and it was interesting to see the difference it makes when the letter is really personal. The teacher we thought would give him the strongest recommendation gave a somewhat generic letter (similar to what jennyp mentioned) stating that he was a strong student, disciplined, natural leader, etc. and listing some of his resume, that we felt could really refer to almost any applicant to a SA (this was his 11th & 12th grade English teacher, really likes son, he's always in the top 3 in her AP class, and she has strongly supported his SA applications - very disappointed in her letter). The letter from his Scoutmaster was amazing and spot on. Scoutmaster had been in the Army and made very specific references to son's character, extra training, leadership style and experiences, etc. and how all this would lead to him being an excellent military officer, with further specific details.
Think very carefully about who you ask for your letters (if you have a choice), because it's not how important they are, but how well they know you in the elements that are important to the Academy, e.g. your leadership style, work ethic.
Whether for the MOC's or the USNA application, read all instructions very carefully and don't rush to complete them so early that you miss including something really important, e.g. Son went backpacking with Scouts in the Rockies (Philmont) for 2 weeks after his junior year and used this experience as the basis for all his college application essays - I was amazed when I read the essays and realized what a life changing time it was for him. Remember it is also really important that your essays show who you are.