Coming from a Linux/Apple/Windows/DOS background- As file manager goes Tracker just doesn’t “get it”. I see the need for a Krusader/GNOME Commander/Explorer/Finder/Midnight Commander/DFM type of file manager. It is a pain to have 10,000 windows open up while browsing though your files. (I know about the right-click thing, it is almost as bad: too many paths that you are not interested in).
Also copy/cut and paste of files would be nice.
Preferences > Tracker > Single Window Navigation.
Maybe it’s you who does not get it? 
The users guide shows how to do all this:
http://www.haiku-os.org/docs/userguide/en/tracker.html#tracker-preferences
Those functions are implemented in the right-click menu. Oh, and the implementation is done in the way you probably won’t need to have two windows open at the same time. Only the source window will do
Agreed, the context menu does display lots of files/directories but at some point of time in the future it would probably get more user friendly.