Place the knobs where you want them. You can get fancy and measure everything or you can do what I do here and put them down and arrange them until they look good.
You also want to decide where you want your power on LED to be located.
Drill out the holes with a 9/32 drill bit.
Here I am using a hand drill and holding the box between my legs. If I was using a power drill, I would clamp the box to my workbench, and not let that drill anywhere near my legs. :)
Some cigar boxes, like this Punch box here, have sides made of pressed cardboard and will drill through much easier than an equivalent thickness of wood.
You can expect some tearout, especially if your box is paper covered pressed cardboard. Some plywood boxes will have little to no tearout and some will have quite a bit.
You can reduce or even eliminate this tearout by clamping a scrap of wood to the inside of the box.
Now look at one of your pots, with the shaft facing you and the solder lugs facing down. This is the right way up for your pot. See the little tab on the left hand side? We need to drill little holes for that tab. That tab keeps the pot from rotating freely if the nut gets a little loose.
Figure out which way your pot needs to face on your cigar box. Measure 5/32nds of an inch from the main hole to find out where to drill the smaller one.
The space inside the cigar box is pretty cramped, and I can't even fit my little ruler in there to measure. So I used a 5/32 inch drill bit and made a mark where to drill the next hole.
Here is my mark.
The pressed cardboard really helps out here, because I can just drill out the hole for the tab by hand.
A test fit of the pot shows that it fits perfectly.
Repeat with the other two holes.
Sometimes I get a visit from Hack Kitty when I'm working.
Now it's time to drill out the hole for the LED. Use a 1/8th drill bit for the 3mm LED. This is going to be just barely big enough for the LED to fit.
It will be pretty tight and you'll have to apply a fair amount of force to get the LED in there. But don't push too hard or it will go right through the hole! If the fit is too tight, you can make the hole slightly bigger by hand twisting the drill bit on the side of the hole.
If you make the hole too big then the LED will want to fall out of the hole. If this happens, you can use duct tape or hot glue on the back side to keep it in place.
When installing the pots, use needle nose pliers to tighten the nuts.
After installing the power LED and the knobs on the pots, here is what the finished amp looks like!