Embed both. For context, I was working on a regulatory knowledgebase. So, I chunked and embedded all the regulatory docs. I asked a question that should have been answered in a particular doc, but somehow the OpenAI model just couldn’t get it right. So, I added the question to the doc itself and re-embedded. Now, the doc comes up when that question (and similar questions) are asked. Based on that, I actually created a Q & A dataset, like yours, with the answers to questions embedded with the questions. In fact, I wrote code to prompt the LLM to create 10 questions for each document and append to that document before it is embedded. Needless to say, this has improved search results on those datasets.
For question-like work embed questions to compare them with context