Hello, Victoria.

Thank you for contacting us.  Assuming you have Safari switched on in System Preferences > iCloud, your bookmarks should be the same on both computers.  This is the job of iCloud.  Any differences which remain hours after the last change, in particular duplicated bookmarks or bookmarks appearing at the root level instead of in their assigned folders, indicate that your iClloud is on the fritz.

Copying BookMacster data from one computer to the other will just make things worse because iCloud will think that you want duplicates of everything.  The fix is to remove all bookmarks and folders from both computers, wait for things to settle down, and then re-populate into the void on one computer.  iCloud should copy to the other computer.  That's the short version.  We also have this long version with more detail.