The QNX System Builder perspective contains a Terminal view for interacting with your board's ROM monitor or QNX IPL and for transferring images (using the QNX sendnto protocol). It also has an integrated TFTP Server that lets you transfer images to network-aware targets that can boot via the TFTP protocol.
Using standard QNX image-building utilities (mkifs and mkefs), the QNX System Builder can generate configuration files that can be used outside of the IDE for scripted/automated system building. As you do a build, a Console view shows the output from the underlying build command.