Unfortunately, Vision Assistant does not currently supports coordinate systems (fixturing as you call it).
The way to do it with the shipping version is to migrate your Vision Assistant script to LabVIEW and manually add the ROI transformation.
NI Vision provides some example code on how to use the Transform ROI function.
C:\Program Files\National Instruments\LabVIEW 8.5\examples\Vision\3. Applications\Rotating Part Example.llb\Rotating Part Example.vi
The next version of Vision Assistant will support coordinate systems, just like Vision Builder for Automated inspection does.
-Christophe