[BScout]

Yes, in Pro Tools you would have to patch the HD MADI to the HD IO.
The S5 doesn't see anything in patchnet other than MADI. What you connect to the other end of the MADI Euphonix interfaces is up to you. If you want to use the HD IO converters you have to get signal to/from it and it does not operate stand alone. So you would have to loop the HD MADI output through to the HD IO output in Pro Tools and then do the same in reverse (signal coming in on HD IO input going through to the MADI input which then goes to PatchNet.)

You have to remember that the System 5 is a Euphonix product and not really an Avid product. It has no direct communication or interaction with Pro Tools hardware. (other than the later addition of Eucon for DAW mode of the console)