Thanks nieldk - I agree it might be problematic to get this working without breaking some DNS queries.

For anyone intereseted, I got TorDNS working by redirecting all outgoing DNS queries to it with iptables. Here are the instructions (only do it if you have a good idea what what all this means, and again it might break certain DNS queries):

Add the following to /etc/tor/torrc:
su-devel
iptables -t nat -A OUTPUT -p udp --dport 53 -j REDIRECT --to-ports 9053

Then restart tor. Check that it's working by going to a tor hidden service like duckduckgo's: 3g2upl4pq6kufc4m.onion.