The Sub-Carrier could transport Mini-subs piloted by individual B1-Series battle droids and autonomous manta droid subfighter.
The mini-subs would exit through tubes located on the underside of the carrier. This was a dangerous maneuver, as Galactic Republic SCUBA troopers could ambush mini-subs on their way out, and there was no way of turning back once a sub was racing through the launch-tube.
The Sub-Carrier resembled a vulture droid in shape, but dwarfed such craft in sheer size and volume. Each carrier was so big that entire skirmishes could be fought on the topside deck.
The Xi Char provided the blueprints for the Sub-Carrier to the Trade Federation free of charge for not being able to figure out how to make the manta droid subfighter transform like the vulture droid.
The Separatist Sub-Carrier somewhat resembles an unused destroyer droid carrier for Attack of the Clones, except it had four legs instead of two.