I'm not sure why you are having the add-ons annoyance and the refreshing problem.  But its better to ask about problems than just be annoyed about them with no possible solutions.  I'm not sure what is causing the problems nor how to stop them.  I may have suggestions as the discussion progresses.

As to organizing book marks, I would suggest doing the following instead of this time consuming and unending work with book marks.  I never organize book marks because I have no reason to do so.

Don't neglect history.  I usually use history rather than book marks.  I create book marks so I will have sites in a permanent form which I can export and won't lose if I get a different machine and use Firefox on it. 

But I find it much more efficient to use history to get to sites and the address bar autocomplete.  I don't have a rule,  Use whichever you want and whichever works best for this or that site.
Open history with control h.
You are in a search field.
Type some or all of what you are searching for.
If, for example, you want to go to The New York Times home page, type times in the search field.  If there are a lot of different history entries with Times in them and the search results show too many entries without the home page being near or at the top, type something like rk times which will very much limit the search. 

You can experiment and see if history entries change their position, depending on how much you use them.  I have a lot of history entries for articles from The New York Times but the home page is the first entry in the history list.  I can type something like times or rk times in the search field, tab twice to the list, and see what is the first one and those below it;.  Press enter on the one you want and the page opens.
You can leave history opened or close it with control h after the page loads.  If you leave it opened, use control h twice to close and o[pen history again, ready to be used for your next search.

I also use the address bar.  Go  to it with control l.
If I type just the letter n for new york, the address of the New York Times appears in the home page.  I wait to hear what my screen-reader announces is there.  I press enter if it is.  If I don't hear an automatic announcement after I type the first letter, I use the read current line command.  If what I want is there, I press enter.

If I type too much, the autocomplete entry disappears and only what I type is there but that is another quick way to open some sites.  Try the first letter or the first two or three letters of things

Try typing the first two or three letters if the first letter doesn't do what you want.  For example, try new if you want the autocomplete to show Newsweek.

Of course, autocomplete will only find sites you have gone to before and I'm not sure how it decides what to show.  Perhaps its based on the most used site that beginns with the letter or letters you type.  Whatever the case, I go to The New York Times site a lot and I would rather type n, wait for the echo and press enter than use book marks or history for that site. 

If you wish, I can tell you how to use the search book marks feature to find one but I'd have to go over it again befcause I never use it.

Gene