When I was writing the commercial starships for Mongoose I had the same question, since there wasn't much on modules for starship use.
the process was simple, build it the same way you would a ship, but you don't need a bridge, or computer, since it has no drives, or advanced systems For pods with weapons, sensors, etc you can add computer, and cockpit for crewmen...or use a system link if you have the stats for that.
I used this method and it turned out fairly well.
Another option for using modules was to fit the carrier ship with docking clamps. once connected you just attach the tonnage of the module to the ships total tonnage.
the main difference being installation. with docking clamps you just use a tug to dock the module to the ship, or install it using a gantry at a starport. instead of integrating the module into the ships computer and power systems....of course you have to add those to the modules if you want the modules to operate independently.
You can bend some of the rules slightly if you make the module an independent system...such as adding weapons above and beyond the normal limits of the carrier ships tonnage.
a ten ton gunnery pod can fit a single weapon such as missiles, or lasers, using it'sown power, and computers...as well as a crewman who rides in his own stateroom in the pod.