The way to align a rifle in a case depends on whether the foam is custom cut or not. If the foam comes already cut, then how you align the gun doesn't matter. Check that the foam contours the rifle's entire body to ensure an even spread of its weight. Alternatively, you may contour the foam around the rifle's body while leaving open the scope area. However, it would help if you endeavored to configure the foam right since that is the most critical factor and not the rifle's alignment.