I don’t recall anyone ever talking to me about how to position bolts and nuts in the things I build. With experience I have made some rules of thumb for myself.
Rule one: Give it some thought. The idea of thread joinery is to hold some assembly together which can be disassembled when necessary. Design to satisfy both sides of that equation.
Rule two: Avoid obstructions to bolting and unbolting.
Rule three: Pay attention to strength needed. Most of the time Grade two hardware will work but in some cases plan for Grade 8. I use mostly 7/16” size stock as the other part of the strength consideration.
Rule four: Pay attention to the security required. Usually I use a split ring lock washer but sometimes Nyloc nuts, thread locker, paired “jam nuts” or fabricated wired nuts to avoid unintentional loosening. Sometimes, in special cases, I place a weld between either the bolt and the assembly or the nut and the assembly and, rarely, both.
Rule five: Think about fail-safe. How many fixation points are really needed for safety? The more the better for holding together but excessive parts make disassembling awkward.
Rule six: How should the bolt be placed? If the bolt is oriented in the vertical plane and only the top side is visible during operation of the assembly, the nut can fall off and possibly not be noticed. However, the bolt can’t fall out. If the nut side is up and visible, loosening might be noticed before the nut comes off, but the bolt will fall out when that happens. Which is better in the particular case at hand?
Rule seven: Lubrication? I like to put anti seize on the threads of most everything I use.