Gerald, I have mentioned this particular volume a number of times before, and it will be quite helpful, in relation to the Union Army steamboats that were used throughout the war. The publication is titled THE ARMY'S NAVY SERIES: DICTIONARY OF TRANSPORTS AND COMBATANT VESSELS, STEAM AND SAIL, EMPLOYED BY THE UNION ARMY, 1861 - 1868, compiled by Charles Dana Gibson and E. Kay Gibson. It was published in 1995 by ENsign Press, P.O. Box 638, Camden, Maine 04843.
As for the Confederate transport and other vessels used, there may be some mention in the Naval Official Records, and there are definitely some also mentioned in volume 2 of the DICTIONARY OF AMERICAN NAVAL FIGHTING SHIPS, though some of these non Naval vessels are actually lumped together with Confederate States Navy commissioned vessels in Appendix 2 of that volume. A quick perusal shows several examples, such as the BEAUREGARD, a Confederate Army steamer used for transporting armaments and troops, in the Louisiana and Red River region.