Transports are free, but must be taken (and squadroned) in pairs. For each pair, the Defender can take 100pts of ships, per the restrictions in their fleet list.
The Attacker rolls a D3 and adds the number of pairs of transports that the Defender takes. They make this many rolls on the chart in the Convoy mission, then makes appropriate choices from their fleet list.
This mission is incredibly variable. With poor rolls, the Attacker would have a few ordnance markers and a handful of escorts. On good rolls, they can have a fleet with several squadrons of escorts and even a few capital ships. I've never had a mission where the Defenders weren't outclassed.