Attaching sill plate to concrete, how do I attach framed wall to sill plate?
Drill a hole, or a recess, into the bottom plate of the prefab wall, so the bolts holding the sill plate to the concrete just slide right in/through. 

Or, drill a similar recess into the sill plate, recess the nut into the sill plate (probably with a washer to spread the load over the thinner wood), and grind/cut the bolt off level with the top of the plate.

Whatever you do, make sure this doesn't compromise the structural integrity of the sill plate or wall (shouldn't) or introduce any potential for leaks or collected water inside the recesses or holes (again, shouldn't, provided the skin of the shed remains watertight and you're not saturating the inside with a hose on a regular basis)