It depends on how related your follow-up question is to your original question.
In your example, I think that your follow-up question about syllable emphasis is a "sub-question" of your original question "how should I pronounce Buddhism?", and so you should post it in the comments. Likewise, in any case where your follow-up question is necessary to clarify some unclear details of an answer or to get a more complete answer, you should post it in the comments.
On the other hand, consider a different example:
Question: "How should I pronounce Buddhism?"
Answer: "Boo-di-sm, and not Buh-di-sm"
Follow-up: "Thanks, and also, what's the etymology of 'Buddhism'?"
In this case, I would say that your follow-up question should be a different question. Even though the etymology of "Buddhism" is very closely related to the pronunciation of "Buddhism", these are fundamentally different questions. In this case, you should post your follow-up question as a new question.
I think it would also be appropriate to comment on the original answer with something like "Thanks. By the way, I posted another question at [link] which is related". This is helpful for everybody, because this makes the linked question show up in the "Linked" section of the sidebar, and thus helps connect people (including the answerer) to questions that may also be of interest to them.
I'm sure there must be some good posts about this over at Meta.SE, but I haven't been able to find any. If you find any of them, post them here - every site has had to deal with handling follow-up questions, so we may as well draw on their wisdom where possible.
There are a number of posts about "chameleon questions" and so forth, but those are more written for the benefit of an answerer who has to deal with a misbehaving asker, rather than for the benefit of an asker who isn't sure what should go in the comments and what shouldn't.