The "Missouri Adjutant General's Report For the Year 1965" on page 461 among the roster of regimental officers of the 3rd Cav MSM affirms that Captain George W. Carey was placed in the command slot of Company B as of 13 July 1864 with date of rank effective that day, and held that position until he was mustered out 16 Mar 1865.
Captain Herman M. Roosa is Carey's predecessor, as he received his captaincy 22 Feb 1862 and was placed in the Company B command slot as of 24 March 1862. Captain Roosa resigned 12 January 1864.
I would assume that during the gap between Captain Roosa's resignation and Captain Carey's filling that position (12 Jan 1864 to 13 Jul 1864) the ranking company lieutenant was in command of Company B. That would be the same man, First Lieutenant George W. Carey.
Incidentally, no post office address is given in this source for either Carey or Roosa, but other Company B officers' post offices are listed as Greggsville and Hamburg, IL and Madisonville, MO.