Thank you for your question.
You are an EU-citizen. That's why your spouse has the right to get a residence permit if you get married. He probably has to apply for it at the aliens department (I'm not really familiar with the Dutch asylum system, but that's how it works in Germany).
It's probably good if you live together. That way authorities might not get suspicious about the reasons why you got married (e.g. fake marriage). But apart from that it doesn't matter where you live or who you live with.