Did you also get a Truss Rod Adjustment wrench?
One of the small Allen keys is for adjusting your bridge - individual string saddle positions.
I have no idea why you would have two other small ones. I assume your S2 SC is fixed bridge, not a trem. Maybe you got a gig bag from a CU24, and the other keys are for adjusting the trem bridge saddle heights and the trem bar sleeve "tightness".