I'll let some else answer your questions about VMWare, but I'll tackle the names.

As I frequently whine to the developers, there really is no such thing as QNX 6; it's really QNX Neutrino, and the 
current version is 6.3. Rob Krten wrote his Getting Started book when QNX Neutrino 2 was the latest version, but most --
 if not all -- of the information still applies.

QNX 4 is a completely different kettle of fish.

Once you have the vmtoold compiled in QNX6, you should just run it in the background like any daemon process.  

It will do a couple things for you.  It will communicate with the host and share time sync info - this means your clock 
in the guest OS will stay synced with the host OS.  It will also share clipboard info - if you cut something in photon, 
you should be able to paste it in Windows or vice versa.  Lastly if you have turned on the mouse grab/ungrab feature in 
your preferences, the mouse will automatically be grabbed when you move over the vmware window and leave without help 
when you exit the window.

You need to run the daemon as root if you want the time syncing feature to work and you need to run it in a photon 
environment if you want the cut and paste and mouse grabbing to work.  I usually install it setuid root and start it 
when I log into photon.

Rick..