In my version of the Kobo Destop Application (ver 1.9 Mar 30 2011) the bookmarks accurately reflect the state of the books on my Kobo. If I read something on screen then re-sync the Kobo open precisely at that place and vice-versa.
So it would seem that the desktop app's bookmarks (at ver 1.9 Mar 30 2011) are neither "bogus" nor "meaningless" in all cases only some particular cases. Now we can think about providing suggestions to "benham" to diagnose his/her original problem.
So, benham, what is the version of the desktop app you use and are you on Windows or Mac operating system? On my mac the version can be found by clicking an "i" in the upper right corner.