Sync will combine the bookmarks on those two devices.

Well, I did the sync and am now in a huge mess. Luckily, I backed them up on both computers and now created a table and copied them all there, so that I can compare. It ain't easy, because I have a lot of them on both computers, but I think it simply doubled up on the laptop - but thins got messy on the desktop as well When I saw that the bookmarks doubled up, I noticed that all the folders were in alphabetical order, then a new list of folders started right under the other. I thought that should be easy to fix - I'll just sort them into alpha order and delete all the duplicates. It refuses to sort into any order! So, I tought I'd do a restore. The first thing that happened (so far I've only done it on the laptop) was that Greasmonkey jumped up and told me that something was corrupt (disappeared to quickly, couldn't read it properly) I opened a couple of bookmarks to see if it works, and then I noticed something. It had re-synced itself! As I backed it up _before_ I set up the sync on the laptop, I presumed that would need to be set up again before it will sync again, apparently I was wrong. I can (and will) restore it again, but I wonder is there a way of avoiding what happened. The problem may be, because some of the bookmarks do appear on both machines, but not all. I was expecting to get a table of some sort, showing what was happening and asking for decisions from me as to which bookmark I wanted to keep, if there was a conflict None of that happened, it seemingly just popped the bookmarks from the desktop at the end of the already existing list and to top it off, It won't even let me sort them. Am I missing something?

It may take a few days for the bookmarks sync to get all your bookmarks arranged completely the same on both devices after the initial Sync process. If you are going to manually sort your bookmarks order, don't have both devices open with Firefox at the same time, and Unlink from Sync on the device that you are doing the manual sort on - otherwise your changes will be sent to the Sync server all too frequently and to the other "active" device (for me I can see changes on the other device almost immediately when I am adding or removing one bookmark).

A few of my tips for "sorting" bookmarks.

1. I do my rearranging of Bookmarks in the Sidebar, not the Library window, and do a "drag'n'drop" to move them around.
2. If you have any horizontal line Separators, the Sort by Name feature stops at every Separator, so if you want all your bookmarks in the Bookmarks Menu alpha-sorted all together get rid of all the Separators before you start.
3. Sort by Name or alpha-sort will be folders at the top, followed by the indiividual bookmarks. It's been like that since day-one with "Places". I am not aware of an add-on that modifies that behavior. We have seen a good number of requests for the folders and loose bookmarks both to be in the same alpha-sort order regimen, but that has never been changed.
4. And last, but most important - do not "push" too many changes, too fast. Open the Windows Task Manager CPU meter and keep track of it as you are re-arranging bookmarks, and let Firefox "catch up" to your changes. By experience, you stand a chance of losing bookmarks or b0rking your bookmarks file if you push changes too fast.

As far as synchronizing Add-ons goes, IMO that is not something to do on the initial Sync process - especially when you have a huge number of bookmarks on both devices. Save your "sync process sycles" for your bookmarks at the beginning. Also, when it comes to Sync for add-ons - IMHO - it is virtually useless for add-ons like Greasemonkey. It's been at least 6 months since I last used Sync for add-ons, but none of the user settings / scripts were carried over to any other device - and I had 4 devices on that particular Sync Account (one existing Profile and 3 new Profiles, as a test of the "new" Sync service) - all got Greasemonkey, but without any "data" from the "existing Profile" I started out with. Bottom line is that each and every add-on that saves prefs or data in a non-default folder or file in the Profile folder has to be specifically made for Sync of its' settings / scripts / data. An add-on like Greasemonkey is useless until the user puts scripts in to it and without the scripts being synchronized the Sync service is wasting your time by just installing the base add-on without transferring your scripts over via Sync. IMO far easier to make a copy of a good Profile and copy it over to another device to make things a close to identical as possible on the 2nd and subsequent devices.