I''ll just offer my thoughts and experiences, not that my way is any better, or worse, than yours.
First, since all of my media from ancestry.com comes into my files as media attached to a source, I find no need to rename the media. I find the media by
1) the People Workspace > Person page > appropriate fact > Source > Media or
2) The Source Workspace > find the source in the left hand panel and contine to drill to the citation is attached.
Since I never go into Media space to find media, I have no need to rename the media. I consider FTM Media as in a big Fibber & McGee closet, but everything is indexed via 1 or 2 above. (For you younger folks, the Fibber & McGee closet was a (hallway?) closet in a radio program I used to listen to as a kid. In every show, there was a moment when Fibber went to open the closet and McGee said "Fibber, don't..." and then there was a huge noise of all the stuff falling out of the closet as Fibber opened the door.)
You aren't clear about who you apply this secondary copy to. Is it every person in your file? Every person you've researched, no matter how related? I only maintain copies of documents/media outside of FTM for my own ancestors (and sometimes their siblings).
As the years go by and I have explored all of my personal ancestry, I find my wanting to continue my work in genealogy by going into an area study and a single surname study and finding my relationship to presidents and famous people (from New England ancestors) and other "fun" pursuits. I only maintain copies of media outside of FTM for my personal ancestors, not the various people I have added in my other genealogical interests. The main reason is simply time. I choose to spend more of my time doing genealogy than "housekeeping".
As for organizing my folders, I am not familiar with Lisa Louise Clarke, but here is what I do:
Separate folder for each MALE line of each female ancestor (ie her father's paternal line).
Paternal grandfather's paternal line
Paternal grandfarter's mother's paternal line
Each generation has its own folde within each surname folder.
and on and on that branch of ancstors go, each generation being "nested" under the generation before.
I had thought about another version of using a master folder for each name, but I found that a bit unworkable, as the census record for an ancestor as a child might be filed under his parent's as an adult - it was easier to find those "conmingled" situations by having one folder in the folder for each couple and then branch out from there to a dad's side and mom's side. That is, until I hit my New England ancestors. Think of the organization as if it were an extension of an ahnentafel. In fact, one could assign ahnentafel numbers to each folder. But, since the ahnentafel numbers would be different for my children and my grandchildren for the same ancestors, that wouldn't work so well.
I do use an alphabetical arrangement of folders for my New England ancestors simply because there are so many and so many generations. I have two main entry points back into New England, which lead to approximately 125 identified immigrant ancestors, but several hundred total ancestors when considering that my New England ancestors stayed there over 200 years. There are simply so many NE ancestral lines, that I am "forced" to use alphabetical arrangements for them.