how do I find out what version of Tor I am running?
dpkg -l tor
question how do I update Tor to a new version?
Update all packages installed:
apt-get update && apt-get upgrade
Update Tor only:
apt-get install tor
If your using the Tor version coming with Ubuntu you may not receive the 3.0.6 update, many distributions use older version (which are still supported and receive security updates). If you want the newest version have a look at this guide.
will this mean shutting my new relay down?
Yes, your relay will be offline for about a minute.