You do not use freighters and cargo holds to transport supplies.
Instead you must use Maintenance Storage Bays.
The order to load supplies is "Resupply from Colony" (this is the same order that any ship is able to use) and the order to unload supplies is "Transfer Maint Supplies to Colony" (specific to Supply ships)
Note the cargo shuttles will still affect the speed at which supplies are loaded and unloaded.
As a quick test I SM a ship with ~8k supplies and 8 cargo handling multiplier and it took ~3 days to load/unload. The same ship with no cargo shuttles took over 15 days