XTC, temporary attached is a screenshot of the RARR civilopedia about "Supply Shipments", hinting in bold letters, that the options "capture shipments" and "Victory Point Scoring" must be enabled, to allow the supply shipments to work properly.
I marked that passage in this post with a red box. If you don´t have that information in your RARR civilopedia, it seems that something went wrong in your download or installation of RARR.
The supply shipments in RARR have eraspecific graphics what makes them more difficult to integrate in a mod than a normal unit. As far as I remember, the eraspecific units can hold up to four different unit flics and pediaicons graphics, but can only be shown by one graphic on the unit_32 file (that is used for graphics in the cityscreen).
Normally the unit_32 file is not needed for the supply shipments, as these units are autoproduced and therefore cannot been chosen in the build-queue, and they are not been garrisoned but changed to gold when entering the capital, so I didn´t have a closer look into the unit_32 file for supply shipments.
XTC, can you please post a save-file with lots of garrisoned supply shipments, so I can see what icons were used in the cityscreen.
A save-file would also be helpful for looking at the terrain around your cities of Palmyra and Viroconium.