I don't think there is a solution to problem 1 because it's working as designed: the Bookmarks Bar is a folder on the Bookmarks Menu and can't be displayed separate from that. Problem 2, however, is not working as designed. Your bookmarks should appear within the folders listed on your bookmarks bar. You might try going to Settings>iCloud, turn Safari to Off, choose Delete from My iPhone when prompted, then after a minute or so, turn Safari back to On to redownload your bookmarks from iCloud. They will reappar on your device after a brief delay while they download.
Thanks for the quick response randers4. I don't quite follow, not sure if you miss understood or if I am.
Let me re-phrase:
On my desktop in Safari there is both a Bookmark Menu and a Bookmark Bar. They are presented as separate, not one within the other.
This is presented as the same on my iOS devises, two separate folders at the same level, not one within the other.
When I save bookmarks to my desktop Bookmark BAR, they are synced via iCloud to the Bookmark MENU on both of my iOS devices. Are you saying this is as designed? That does not make sense.
Also, when I just created a bookmark on my iPad, inside a newly created Bookmark Bar folder, it synced to my iPod touch as I would expect, in the same manner as it was on the iPad, creating that folder with bookmark in the Bookmark Bar of the iPod Touch. However that new test folder I created under the Bookmark Bar on my iPad did not sync in any way with my Safari on my desktop Mac.
All of this seems broken to me.
I understand what you are saying. I use Safari on OS X Mountain Lion too. What I'm saying is that Apple designed bookmark syncing to iOS devices to work as you are seeing it. On your Mac, bookmark collections like the Bookmarks Bar and Bookmarks Menu are listed separately from the Bookmarks folder list. On your iOS devices, they appear as folders inline with other bookmark folders. This can't be changed.
Like you, I prefer to use the Bookmarks Bar. What I do is tap the Bookmarks Bar folder on my iOS devices and leave it like that; then every time I tap the bookmarks icon in Safari that will be the view you see. I just igonore the fact that there may be duplicate folders in the complete bookmarks list.
From your experiments on your iOS devices it appears that the problem is with bookmark syncing on your Mac, not on your iOS devices. Try going to System Preferences>iCloud, uncheck Safari, restart your Mac, then recheck Safari again and choose Merge with iCloud when prompted. Then on one of your iOS devices go to Settings>iCloud, turn Safari to off, choose Delete from My iPhone (iPad), then after a minute or so, turn Safari back to On. Open Safari on the device and allow it to redownload your bookmarks and see if the links appear inside the Bookmarks Bar folder now. If they do, repeat this on your other iOS device(s).
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:
Get Bookmark Add-ons
Feeds (folder with items in it)
Unsorted Bookmarks (folder empty)
Is that part of my problem now?
You know. I just saw that my test folder that I created on my iPad in the Bookmarks Bar just appeared as an addition on my desktop Safari along with my other Bookmark Bar items. So that seems possitive in some way that there is something going on as I would expect it. If I could just get the Bookmark Bar items from my desktop to reciprocate.
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?
Yes. All of my Bookmark Bar folders on my iOS devices contain the same links as my Mac. If I add or delete a link from the Bookmarks Bar on my Mac, seconds later they are added or deleted from my iOS devices.
The problem does seem to be on the Mac side of things, it is not uploading changes to iCloud properly. The only other thing I could suggest is going to Settings>iCloud on your Mac and signing out of your iCloud account entirely. When you do, you will receive multiple prompts about when to keep data on your Mac. Choose delete to all of these prompts; the data will remain in iCloud and will reappear on your Mac when you sign back in.
Then restart your Mac, sign back into your iCloud account and recheck your sync settings. Your data will reappear on your Mac but may take several minutes to fully download.
Sometime that will fix things when nothing else will.
If the problem persists, I'm not sure what else to suggest. You could hunt around for other suggestions, such as the ones in these posts: https://discussions.apple.com/thread/3929126?start=0&tstart=0 and https://discussions.apple.com/thread/4010846?start=0&tstart=0.
I tried your suggestion and that did not work, but the answer at the first link of the two you provided did. That did it.
Although, I would add for anyone looking at that, after fixing the problem, and importing my Bookmark Bar items back in, they were imported into a separate Import folder, not in my Bookmark Bar where they came from. It took me a while and several tests to figure out the way to handle that is simply to move (highlight, grab, drag) the folders and items in my imported folder up and into the Bookmark Bar folder. That worked.