Hello Miae,
Most processes such as transport by truck, includes empty return trips in the process.
If the chosen transport process does not include empty return trips then consider if its realistic that the ship will return with no cargo. In the example of a container ship, it will almost never return with no cargo.
If you are convinced of the empty return trip, then i would take an existing process, investigate the fuel use per tkm in the unit process, calculate the fuel used for an empty return trip using secondary literature, and calculate the amount of "tkm" you would need to use that amunt of fuel. Remember to allocate only a part of that fuel use to your return trip.
This is a slightly complicated exercise, but im sure you can do it. Good luck.