Sure thing. I hope this isn't too long.
I use 2 different types/styles of hinges, depending on if I want the lid to open 180 or 90 degrees. The process is the same for both. They are all sized in millimeters with the small 90-degree ones being 5mm diameter width and the 180-degree ones I use are 8mm, 10mm, and 12mm. diameter width depending on the thickness of my box sides. When using the small 5mm 90-degree hinges, you have to put a chamfer on the back of the box bottom and lid, or it won't open properly.
So, I have bought millimeter drill bits just for the hinge holes. Even though the drill size matches the hinge diameter, they can still be a tight fit. I like a snuggish fit but not loose as I test fit the hinges several times before final assembly, and they can't get stuck in the hole. I sometimes need to ream out the holes with a small dowel and small piece of sandpaper wrapped around it.
I build all my boxes complete at first and then saw off the lids.
First, I cut and glue up the 4 side pieces. I have a rabbet sawn into them which I inset and glue the bottom into. I try to get all VERY square.
***Now before I glue on the piece which will be the top, I drill holes for the hinges***
Once those holes are drilled, you can glue on the box's top piece, square up and pre-sand the box a bit. The holes are complete and will reveal once the lid is cut off.
Before the lid is attached, I select which will be the back side of the box and I will drill down through that piece creating holes for the lid's hinges AND the bottom's hinges at the same time. I put the back of the box against my drill press fence, being careful to get the hole's set back the correct distance from the box's rear edge. You don't want the hole too far set back from the box's back if you are using the 180-degree hinges or they won't fit right. Set back distance is usually on the hinge install directions (it's usually a bit less than half the barrel's distances when fully opened). The smaller 90-degree hinges set back distance isn't so fussy, but you will have to put a 45-degree chamfer on the lid and bottom up to half the hole's diameter. You don't want these holes set back too far or you will have large chamfers. Determine how far in from the sides you want the hinges and mark it. Drill the two holes. ***To be clear, you will be drilling down through the entire lid's back and into the bottom piece at once. Yes, there will be a void in the lid above where the hinge will be set, but that will never be seen as the glued-on top will cover it***.
You will need to measure down the back's side and mark where the lid will be cut off at. The hinge hole depth will be a bit below that (adjust for some clean-up where the lid is cut off). Once the lid is off, if the hole is a little too deep, you can add a small piece/shim of wood to bring the hinge up level with it's hole. If it isn't deep enough, carefully redrill it a bit deeper as needed. That should be easy if the drill press fence wasn't moved!
Since you are drilling two holes at once, the lid's alignment will be perfect to the bottom.
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