The correct way is to run a complete set of current carrying conductors in each pipe.
As for the equipment bonding conductor it can be sized to each set of conductors in each pipe
250.102(C)Where the service-entrance conductors are paralleled in two or more raceways or cables, the equipment bonding jumper, where routed with the raceways or cables, shall be run in parallel. The size of the bonding jumper for each raceway or cable shall be based on the size of the service-entrance conductors in each raceway or cable.
