TS4001 iCloud Syncs my Desktop Bookmark Bar items to my iOS Bookmark Menu, folders only

I have all of my bookmarks in Safari on my desktop (OS X 10.7.5) via the Bookmark BAR - I have them organized in folders for ease, and I like it that way.
When I use iCloud to sync Bookmarks to my iOS devices (iPad Retina and iPod Touch, latest iOS), the result is that I end up with a series of bookmark folders in the "Bookmark Menu (not the Bookmark Bar) that duplicates bookmarks and folders that I have on my iMac desktop in the Bookmark Bar.
Problem 1.  I don't want them in the Bookmark Menu on my iOS devices, I want them in the Bookmark Bar so I can use them from the bar.
Problem 2.  Even if I wanted to use what ends up on my iOS devices, I can't because none of the bookmarks in the folders are there, only a series of folders.  The only actual bookmarks that are on my iOS devices are those that are not in folders - and again, those few are in the Bookmark Menu, not the Bookmark Bar.
Can anyone help with this?
iMac 27-inch, Mid 2011; 2.7 GHz Intel Core i5 running OS X Lion 10.7.5
iPod Model PC544LL/A; version 6.1.3
iPad Model MD515LL/A; version 6.1.3

So what you are saying is that if I save a url on my desktop Mac as a Boomark Bar item, it SHOULd sync to the Bookmark Bar on my iOS devices?  That was the issue I was complaining about.  It was not.  Please confirm that because I am only assuming that from your last paragraph above.
As for the whole duplicate thing, from my searching the forums today I realize that is a common "issue" people are complaining about - that their bookmark bar items are also showing in the bookmark menu.  I think that is what you were referring to.
So I did try your set of steps in your last paragraph above and they did not work.  In fact, nothing seemed to sync except the test Boomark Bar folder addition I made on my iPad which synced to my iPod touch.  Other than that, nothing else synced from my Desktop - neither in my Bookmark Bar or my Boomark Menu.
Posbily related - Unforntunately, becasue I was having this problem earlier and also had noticed the whole issue with the fact I had all of the same folders on my Desktop Bookmark Menu as I had in my Desktop Bar - I tried to solve that issue by deleting all of the items under my Bookmark Menu, and now I do not have anything in that folder except:
Recent Tags
Recently Bookmarked
Get Bookmark Add-ons
Feeds (folder with items in it)
Unsorted Bookmarks (folder empty)
Is that part of my problem now?
Thanks,

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