I think I'll reply to myself here since nobody else did.
Yeah Will, what you want is to install the shakes or the shingles over the sheathing itself, not over old cruddy shingles. it of course depends somewhat on the condition of the underlying siding or sheathing. If its clapboard or board and batten type, put felt paper over it as a vapor barrier and use preasure treated wood shingles or shakes or pre primed ones. The shiplap of the siding should be enough to create ventilation for the back of the shakes. Shingling is best done from a clean slate whether its on a roof or a sidewall.
You mentioned a long time ago that the roof under thsoe layers of asphalt shingle was composed of wood shakes so you probably oroginally had a house that was clapbaord with a somewhat primitively installed shake roof, since you didn't say they were installed on spaced sheathing but rather the rafters themselves. My recommendation for doing the roof is to take all the old layers off and resheath with plywood if youre gonna use asphalt shingles and with 1x4 spaced sheathing members, spaced at the same distnace on center as the shingle or shake weather exposure, if you're gonna do cedar shakes.