If you are replacing the piston, I think the new one will be marked. If you want to re-use the old piston and its still on the rod, mark it with a scribe or a center punch.
If you are trying to re-use the old piston, be sure your rings fit the piston. Parts book shows 'early' and 'late' but fail to say that early is .096 width compression rings and late is .063 width.
As far as the rod goes, the oil hole goes toward the camshaft. This should put the marks you see on the flywheel side.