The problem introduced by your post is that Ed Singeltary and John L Manous actually lived in Morgan County at this time. Both appear on the 1870 census and although young, they would have been old enough to have been in military service during the war. Singletary only appears on the 1870 census, but Manous evidently lived in the area for many years afterwards. My best efforts have produced nothing on either one in an Alabama command, and no postwar record, such as a pension application or veterans census entry.
There are a few possibilities for unidentified state and/or Confederate service. First, the Governor Watts attempted to reorganize the Alabama militia under the legislature's act of August 1863. Since counties north of the Tennessee Valley were occupied by Federal forces, no organzation could be attempted there. Counties bordering the south bank of Tennessee River were under threat of incursion, and little could be done there. Governor Watts appointed R N Weldon of Decatur as his special aide for Morgan County, but there is no evidence that any 1st or 2nd Class Militia organized in that county.
Second, a number of companies organized in Morgan County during the last two years of the war. We know little about most of them except from Federal prisoner of war records. Some of the most difficult to follow are companies of Stuart's Cavalry Battalion, assigned to Col Josiah Patterson of Roddey's cavalry command. For that matter records of all Roddey's units except Ferrell's Georgia Battery are incomplete, so these men could have enrolled in any of them. It's also possible they could have joined one of the twenty-some odd companies assigned to Hardie's and Barbiere's (Davenport's) Reserve Cavalry Battalions. Most company organizations are recorded adequately, but we do not have anything like complete rolls for them.
Third, an even more shadowy alternative would be W W Lowe's 13th Alabama Cavalry. Evidently Lowe raised a number of mounted companies in north central and northeast Alabama which operated in that area during 1864-65 and perhaps a little earlier. In April 1865 Croxton's Federal cavalry encountered and paroled a number of them on their way east across the state. The unknown force assembled by Brig Gen Hill that Croxton defeated at Munford AL probably included some of Lowe's cavalry and other semi-organized units.
I'm still doubtful that Amos Chaffin could have been a officer and see no possibility that he enrolled in a Georgia unit. However, it's all quite interesting, and I appreciate the opportunity to explore these possibilities.