One for PaulThe Good Shepherd, Paul, and Silas are all figures from Christianity, in which three is a significant number. In the song, that significance is shown in the three sheep mentioned in the chorus.
One for Silas
One for to make my heart rejoice
Interestingly, the chorus itself appears in the song three times, and there are three things to be avoided: "the blood-stained bandit," "the long-tongued liar," and "the gun-shot devil" (at least those are as I heard them). So there are multiple instances of groups of three.