I've asked a question and someone answered it. But inside the answer, there are some questionings, like "I'm not sure I understand your code here...".
Should I attempt to answer the questions of the answer (which could lead to an even better answer) or is this against Q&A principles? If yes: where (comments of the question, comments of the answer, another question, chat, s-mail, ...?)
When you go to comment on an answer on the main site you are prompted with:
Use comments to ask for more information or suggest improvements. Avoid comments like "+1" or "thanks".
If by answering the questions in their answer, in the comments, may improve the answer, I would say it falls under "suggest improvements". Whilst you're not saying something like 'you may want to use X rather than Y', you are instead clarifying the areas of doubt with the aim for a better answer.
I'll be honest, most of the time I just comment without thinking twice about the rules, if someone wants it gone it'll go.
Should I attempt to answer the questions of the answer (which could lead to an even better answer)
To me, the point of the question/answer format is to ask a question and then get an answer. If the answerer is saying things like "I don't understand this..." then the best place to explain is in a new question. We call this process iterative reviews. If you do it, please link to the first question from the second question.
In an iterative review, you should make some changes to the original code, taking into account the feedback you received. Perhaps you can update the code or add code not previously included. For feedback that you ignore, please explain why you are ignoring it, either as code comments or in explanation after the code in the question. As comments if you think that it should be in the real code; as explanatory text if you think it shouldn't.
Note that there are things that should be put in comments. For example, if you want to post that you did not understand the answer, that makes for a constructive comment. Then the poster can update the answer with more explanation.
The rough rule of thumb should be: do you think that the comment is only relevant to that specific answer or not. For example, if someone says, "I don't understand why you created a separate object for this", then you might post that explanation in a new question. Then all potential reviewers can respond to it. Same thing if you left out code that would be helpful to reviews.
