Steamboat traffic on the lower Missouri River was pretty much totally disrupted during the war. However, many boats which had previously operated on the Missouri River were taken by their owners to other rivers in the south to prevent them being confiscated and used by the Federal Gov't. The boats which remained in service were used primarily in transporting Gov't freight, supplies, and troops.
I don't know where you live, but if you are anywhere close to St. Louis, you might try doing a little research at the Herman T. Pott's Inland Waterways Library which is contained within the St. Louis Mercantile Library operated by the University of Missouri--St. Louis. They DO have a database of microfilm containing records of licenses issued to steamboatmen from 1852 onward. You can read more about what they have by going to http://www.umsl.edu/pott/pguides/Officer.htm
Happy Hunting...If you find that he was on a boat (boats) that operated on the Missouri River, I would be very interested in hearing about your findings. If I can be of assistance, please contact me at steamboatgranny@yahoo.com.
Best regards,
Maggie Gilbert
"steamboat granny"