I still haven’t worked out how to set up the HORM but I have managed to work out the following; because the system uses Windows 7 Embedded, I configured the VI to be saved to the Start Up file. This will make sure the VI will pop open and start running as the system starts up. The second thing, which is very important and useful, is deploying the VI for the Compact RIO and has it run on start up! This was actually quite tricky to find but once I figured it out it was really quite simple.
Under the RT target will be a section noted as Build Specifications. Right click and select New Real Time Application. Add the source file of the VI developed to control the VI. It is noted that the destination file for the Compact RIO is set to c:\ni-rt\startup. This appears to save the VI in the start up folder of the Compact RIO. The last step is to Deploy the system.
I hope this has helped anyone else struggling.