Ask YC: Proper way to ask seperate questions in comments?

Just now, i had to ask myself what to do when i were commenting on http://news.ycombinator.com/item?id=138249 .

Basically, i had two unrelated questions to raise for the same article. Should i have done it the way i did, asked both questions in the same comment or should i have asked them in different comments to branch two different discussions.

What is the etiquette?