There are two kinds of cut-outs.

If you are speaking of a circular cutout, it is intended, on longer stroke engines, to clear the rear bearing/crankshaft counterweight (The backplate usually has a level surface on top, to allow piston clearance.). The rectangular cutouts (with rounded corners), are to allow better passage for fuel/air mixture to a bypass.

In side exhaust engines, the boost port bypass if often masked by the piston skirt. Some engines with long skirted pistons, Irvine FE, have a rectangular hole in the piston and a "bulge" on the side of the crankcase, for "feeding" this intake port.

If you can send a photo of the piston, as well as the engine, it will be easier to tell you which way the piston should go.