On November 10, 1862, a Confederate Navy paymaster approved a pay voucher of $12.50 to the Mount Pleasant Ferry Company for the transfer of 52 seamen and their baggage to the Indian Chief. This would be in keeping with its duty as a temporary home for sailors awaiting transfer.
In 1863, the Indian Chief's role expanded when it became an auxiliary to serve as a workshop and assembly platform for Confederate torpedo boats..
On August 24, 1863, Flag Officer J.R. Tucker ordered Lt. Dozier to have "as many boats fitted with torpedoes as you can hoist up to the davits of the Indian Chief and have them ready for service." It would seem W.G. Dozier was also put in charge of torpedo boat operations as he is mentioned as "commanding special operations."