When looking at the description of ADE it appears that it supports synchronizing bookmarks yet I have not been able to make this happen. I have ADE on a Macbook and on an iPad and the bookmarks created on the MacBook are not transferred to the iPad. Is this feature being misrepresented on Adobe's website??
Looking at the description of ADE, it mentions bookmarks, but mentions that while an ebook without DRM can be copied between machines, the bookmarks stay with the original machine. So it may not have the ability to share bookmarks. I think you also need to download an ebook to each of the platforms, rather than have it happen automatically.
We've got a bit spoiled by the way that iBooks and the like share books, mail and the like across all your Apple platforms, based on your Apple ID. However, there isn't an equivalent system between Apple, Windows and Android platforms (wonder why....?), so there isn't an OS process to manage this.
Hate to disappoint you.... Maybe there is a way to do this, if the bookmarks, etc., can be exported to a file and transferred to the other machine. But without a backroom system to pass things around, it could get messy with changes on different machines at different time.