bookmarks overwritten

I use a lot of Bookmarks as part of my work. I have important customer sites listed in these bookmarks. My work requires I use Linux desktops as well as my Mac and a MS Windows 7 virtual machine. I use X-Marks to keep bookmarks synced between OS X, Linux, and Windows without ever having an issue. When I make a change or add a bookmark and run the sync from the X-Marks preferences, I see it on my other systems as soon as they sync. I also can access my bookmarks on a web site to restore if need be. As soon as I add iCloud bookmarks sync in to the mix though to get my phone and iPad synced it all goes to s#!t. This really ticks me off and I am now having to, again disconnect my iPhone and iPad from iCloud bookmark sync for a several hours until my changes on the Mac become the default iCloud set. This gets old fast......

Anybody have a good solution to this issue? Anyone know of a tool to edit and sync iCloud bookmarks?

Thanks!