How to present documents to the Home Office

[Ekaterinas2016]

It didn't cross my mind before and I know I'm probably going crazy awaiting decision on my (not straightforward) case, but...
Home office requested additional proof of residency and I provided the proof by alternative means because I wasn't able to produce the documents they asked for (being non-EEA family member housewife non-student and not on benefits leaves not much evidence to provide=)
Anyway, I rely heavily on Cover letter I wrote
But by some stupid reason, I put in in a transparent file on the outer front side of the folder. I thought it would catch attention and they won't miss it, but now I think it would be better to put it INSIDE of the folder
A bit stupid question really, but are there any rules of how to present documents to Home Office?
Folders/no folders, files/no files? Do they look into the original folder or a secretary may be removes the documents and handle to the case worker?
Silly thing, but I just wish they actually saw the letter because without the explanation it's a refuse

[bruteforce]

You are overthinking, they will look into envelope and will find all your documents, whether in or out of folder.

[Ekaterinas2016]

You are overthinking, they will look into envelope and will find all your documents, whether in or out of folder.

Thank you for the answer
And I really hope so! May be I just need to calm down. I was close to sending the copy of the letter to their email address, just to be sure, but I'm afraid it will confuse everybody...
I remember when I applied for residence permit in the past the solicitor said that Home Office doesn't like folders, but I don't recall exactly what she said