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I'm talking small wood screws. I place and mark the hardware carefully and mark the center of the hole with a sharp awl.
The problem comes about with small bits like 1/16 and 5/64 and 3/32" walking a little bit because of grain in the wood - it goes OK if the desired location is between grains but the thin bits are limber enough that they wander to the side by almost a bit diameter if the desired spot is on a grain ridge. As the grain is never perfectly square the holes move by different amounts, on small hardware a 1/32"-1/16th" wander in the center of a hole is visible. This is with a drill press, Hand held is worse.
I have seen the so called VIX-type bits that have a spring loaded tapered nose that fits into the hole in the hardware to center the bit, as you push the nose retracts and the bit centered in the holder drills the exact center since it is guided and cannot bend, it enters precisely in the center of the hole in the hardware, effectively using the hardware as an exact template. They feature replaceable bits held with an Allen set screw and come in a variety of sizes ranging from #3 to #10 screws. The slots in the sides of the nose piece are for cuttings ejection.
I tried one set from Amazon with 7 bits for $15. An import as you can guess. They were terrible from the get go with several machining errors and spring noses that did not work or bound up. Sent that one back and ordered the smaller set on left from VIX, a US maker whose trade name is widely used. Cost $37 for a set of only 3.
I got a set for #3, #5, and #9 screws. with 5/64, 7/64 and 9/64th screws for small work. They sell sizes up to ones for doing door hinges with 1/4" drill dia.
So it appears to work well. I lay out the location and tape the hinge firmly to the box leaving one hole exposed... drill and set the screw and remove the tape and do the other holes on the same side. Then do the opposite side with the box halves clamped together. precisely. For my small box I used a hand drill.
The more expensive ones seem to work well and though more expensive have seemed to solve my problem and in the end are worth it for the personal satisfaction and lack of hassle. The hole seems always centered perfectly in the hole in the hardware guide, even in difficult grain.
I guess there are other name brand copies, from Snappy, INSTY and Bosch that might work well, but given the problems with the low cost no-name entries I decided to stick with the namesake from S.E. Vick manufacturing. If you want the original, which is what I'm recommending, get the ones made by S.E. Vick Manufacturing. Beware that VIX is a trade name but it is widely violated in product listings on Amazon, for example.
This is the set I like:
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1
but they are also sold separately as well as the set of three above.
I used a drop of oil through the cuttings ejection slot to help the bit turn smoothly in the sliding nose pieces. This is because the sliding nose piece is a close fit to both the bit and to the holder. It seemed to help, I don't think it contaminated the wood in a bad way that won't be covered by the hardware.
Example 5/64" hole in hasp:
