Hi again Jake,
For the SIII device - in Chapter 11 Configuring SIII Devices doc table 11-2 (Note1) and table 11-3 show Fast AS as the only method available under the Remote System Update scheme, so yes with this arrangement I wouldn't need an external controller (which is what I want).
I read the thread you contributed to here:
http://www.alteraforum.com/forum/showthread.php?t=5280&highlight=remote+upgrade+stratix+iii The Remote Update Scheme seems to allow the overall hardware and functionality that I would like but I don't want to use a Nios processor - is it relatively easy to have a state machine take the place of the Nios - I see an example (not yours Jake, another one. I think yours may use Nios but I could be wrong) in the shared material section but I havn't looked at it yet.
stephen