Alice this link is a wonderful start!!
I will track down this book and see if it lists any NARA Record Groups for this information.
Dear Mr. Webster,
Thank you for posting your request on History Hub!
We searched the National Archives Catalog and located 347 record series relating to transportation during the 1860s, the majority of which are in the Records of the Office of the Quartermaster General. While it is unlikely that NARA has cargo manifests for every single voyage, there may be some records relating to contracts between the War Department and private vessels to transport supplies. For more information, please email the National Archives at Washington, DC - Textual Reference (RDT1) at Archives1reference@nara.gov with full details about the ships and captains you are researching, to include where and when they may have operated.
Due to the COVID-19 pandemic and pursuant to guidance received from the Office of Management and Budget (OMB), NARA has adjusted its normal operations to balance the need of completing its mission-critical work while also adhering to the recommended social distancing for the safety of NARA staff. As a result of this re-prioritization of activities, you may experience a delay in receiving an initial acknowledgement as well as a substantive response to your reference request from RDT1. We apologize for this inconvenience and appreciate your understanding and patience.
We hope this is helpful. Best of luck with your research!