We went with making each pallet a resource with a production calendar of half a shift each. Labor reporting is the easy part letting the system split actual hours based on the to job's different running rates. The hard part is scheduling.
If you always run parts with relatively equal run times together it's a bit easier but not much. When determining an operation's running rate, the load and unload time is negligible. However, if the other pallet is empty that time now adds to the part's actual cost.
How long a job takes to complete is totally dependent on what's running on the other pallet (or not running). I don't know of a perfect answer.
Greg