So I've figured it out, while at the same time hitting another problem, but I've managed to get things to boot, - so here's the procedure I used / solution for posterity (or for the next time I forget).
I booted off a Workbench 2.1 Disk and had another floppy with HDToolBox and the "Dummy-Handler."
Using HDToolBox (which seemed to automatically recognize my GVP controller. I've heard of some having to go through the shell and call "HDToolbox gvpscsi.device" or some such - since I didn't have to do that, not exactly sure)
In HDToolBox with the appropriate drive selected - click Partition Drive
Select the boot partition, in this case "UNIX_Boot" and then click on the advanced options check box.
Then click on "Change…" (just need this to get this information). (This may be greyed out, but still readable. I originally applied things incorrectly, so this was modifiable as Custom file System was selected. After I applied the "Dummy Handler" correctly, the file system shows "UNI\00" and the identifier is now greyed out, but readable.) For a Unix Boot partition the identifier should be 0x554e4900. Just need this info for adding the handler. Click Cancel to go to the next step.
Click on the "Add/Update" button. In Add/Update click "Add New File System…" It asks for the location/filename of the new file system - for me it was "UTIL: Dummy-Handler", will be different depending on where you have it. Then click on ok.
Next will be a prompt for the DosType and version for the File system. Here I put that identifier that I got earlier, 0x554e4900. (I left the Version and Revision values at 0 as I didn't know what they should be.)
Click OK to add the file system. Then click OK to leave the "Add New File System…" window, and OK again to leave the Partitioning window.
At the Hard drive preparation window - "Save Changes to Drive" should be clickable. Click on this to write the new information to the drive. Then Exit. That should be it.
It never looked like my floppy disk was accessed to read the dummy-handler. However, it did work. I also used a RDB archiver to read the drive before and after I applied the dummy handler, and the RDB was larger after the application.
The mistake I made previously was that I selected "Update File System…" This had me applying the handler to the only file system listed which was the "International (FFS)" file system. I presume this meant that when going to boot the Unix Boot partition - while the information was there, it was under the wrong File System ID. I may have also tried "Add New File System…" but again, not sure what the ID should be - left it the default which would have been the same as the FFS already installed.
So that allowed my Amix Boot partition to boot. Of course now it boots directly into a Kernel Panic, but that's another issue for the thread I originally posted - Booting Amiga Unix on a GVP controller.
Thanks for your helps guys.
Mack