Well obviously.Ask the head instructor if...
- Unsure about "something" - gonna have to be more specific what "something" is
The top instructor is always the best person to ask if you're unsure about how the dojo is run as their answer will be the ultimate answer, that's how I see it.
- Unsure about how the dojo is run - I'm going to assume that you mean you try the dojo, and there's something that raises a red flag for you. In this case, bring it up with the head instructor. If there's something that isn't right, he needs to know. If it's his idea, then you need to go. (Alternatively, he may explain why you shouldn't be worried. For example, if you expect to spar starting at white belt, but they start sparring around 6 months in, that's not bad. If they start sparring 5 years in, that's bad.) Alternatively, you can ask the person who gave you the red flag (deal with it one-on-one) or ask the other students/staff if that situation is normal.
Requirements for promotion would fall under the category of "unsure about how the dojo is run" but if you want to talk about it specifically then it would make sense to list it separately. If you want to earn rank I don't see why there would be anything wrong with asking about requirements. Where you talk earlier about stuff that raises a red flag that could in some cases apply to stuff about rank and promotion, for instance if you haven't been promoted and more than a reasonable amount of time has passed. Lets say it takes you 8 months to be promoted from 2nd Kyu to 1st Kyu. Now, you've been at 1st Kyu for more than a year and you still haven't tested for or been promoted to 1st Dan. At that point you probably should ask about it, assuming you want to be promoted to 1st Dan.
- Requirements for promotion - this depends on how subjective promotion is. At my school, you can ask me the requirements, because they're consistent curriculum items. At other schools, you may need to ask the head coach, because his opinion is the only one that matters. Some schools it's bad manners to ask.
I don't see why it would be bad manners to ask about promotion requirements. Demanding to be promoted would be bad manners not to mention downright disrespectful but asking about promotion requirements is not the same ask demanding to be promoted so I don't see why that would be a problem.
Even how instructors do techniques can vary, especially considering the fact that instructors are more advanced, when you get to be more advanced you start developing your own style. So as you said, if you're unsure it would be best to ask the top instructor as his answer would be the ultimate.
- How a technique is done - in general, ask the closest instructor. You don't want to ask another student, because they may give you wrong information. If you're not sure of what the instructor says, or if different instructors give you different ideas, then go to the head instructor for his opinion.