John,

In Joanne Chiles Eakin's landmark 1995 work "Missouri POWs" (the real title is about three lines long) there are two entries in the Union military prison ledger that seem to match the information you gave for two men of similar names. I think the following prison records reflect two different Hamilton men both captured at different times in Lewis County, MO.

These records say:
--Guerrilla William Hamilton of Porter's command was captured by Union military in Lewis County, MO 14 Oct 1862, sent to Gratiot Street Military Prison in downtown St. Louis, and transferred from there 6 Dec 1862 to the Alton, IL Military Prison.
--Guerrilla William P. Hamilton of Porter's command was captured by Union military in Lewis County, MO 22 Sep 1862, was sent to either Gratiot Street or Myrtle Street Military Prison in downtown St. Louis, and was transferred to the Alton, IL Military Prison 5 May 1863.

That is all it says. Some prisoner records tell what happened further to prisoners, but there are no such indications for these two records. Colonel Joseph C. Porter was commander of both the 1st and 2nd Northeast Missouri Cavalry Regiments, if memory serves. The Confederacy considered these men as soldiers under the "Partisan Ranger" Act of about April 1862, Richmond, VA. Porter's men, recruited in northeast MO at or near their homes were not recognized by the Yanks as regular Confederate soldiers, but considered as guerrillas. Fortunately, they were not executed as other proven guerrillas were (under Dept. of the Missouri edict) unless they were found to have violated the laws of warfare by fighting while still under parole or violating an earlier oath not to bear arms against the U.S. A large number of Porter's men were captured in northeast MO during the summer and fall of 1862, and Colonel Porter had a difficult time getting some of his recruits through Yankee lines to the rest of the Confederate army in AR. Many of Porter's men died in the St. Louis area prisons during the autumn of 1862 and winter of 62-63. Many of those that died in prison are now interred at Jefferson Barracks National Cemetery, and I recommend you contact them to see if they have a record on one or both of these Hamilton men.

I hope this helps your quest.

Bruce Nichols