Thin sheet stock can be a problem because as the counter sink is cut, the original hole drilled for the screw
in it is usually enlarged. It can wander a bit from the hole in the wood.
On thin sheet metal like a toe plate or patch box, I've drilled the hole for the screw in the metal first where it needs to be,,this can be done off the gun stock.
Then clamp the metal part in postion in it's inlet.
Now,, assuming the metal is 'sheet metal' and the inletting is close,,meaning there isn't a void under the hole you just drilled,,,I then countersink the hole to the depth I want.
As the hole countersink is cut,,the point of the countersink will cut a perfect center in the wood below it for the screw hole. That center cut into the wood below it ends up being where the center of the screw hole needs to be.
Then I take a drill of the correct size for the screw I'm going to use. I take the point and grind it to a sharp narrow point. It looks kind of like a piloted drill. The small diameter sharp point will follow the center cut from the countersink nicely and put your drill right down in the center of the sheet metal hole.
I did at one time first use a small diameter drill to center drill then follow up with the correct size drill for the screw size. But doing it once is better I think. Less chance of going off the mark.
I do this free hand while the gun or other project is in a vise. I usually use an electric drill, though I have in the past used a hand rotary drill.
You have to eye ball it to make sure you're at 90degrees to the surface like any other work done w/o the use of a mill/drill machine set up & levels,,but other than that it works out great.