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Mainly you just screw them down to the bed. Actually, you don't even have to screw them down, but if you don't it will probably slide around unless there's a ton of stuff in it.
If you do a cross the bed version, there are J shaped bolts that grab the lip of the top of the bed and just put nuts on and tighten down. No need to drill holes.
I drilled a hole through my toolbox and through the rails and bolted it in. I had the J-shaped clips but they didn't work too well but my toolbox is heavy and has a lot of stuff in it.
depends on the box. i have a cross bed so i just have j bolts. my brother has a chest so it bolts to the bed but he uses his bed extender to hold it at the back of the bed