First, I'm not yet a cap-and-ball shooter, so take my words with a LOT of salt.
From what I remember, though, the half-cock notch is used to fill the chambers (and later to cap them), but not to tamp them. When the hammer is down, the topmost chamber aligns with the barrel and the bottom-most chamber aligns with the rammer.
So, again as I recall, one half-cocks the hammer to load the chamber(s) with powder, wad and ball. Then one rotates the cylinder until each of the filled chambers, in turn, locks into place beneath the rammer before actually tamping. I've been told this ensures accurate alignment and prevents a lot of seating problems.
But again, take my words with a lot of salt.