All the builds you pull down from the Downloads page:
Should come packaged with an executable Tomcat you can run via the threadfix.bat or threadfix.sh (as long as you have a suitable 1.7 JDK)
Upgrades between milestone (and RC) builds aren't tested in the same way that upgrades between stable builds are, but you should typically be able to deploy a new version and either copy over (for HSQL) or re-point (for MySQL) the database. This document generally describes the process:
(with the caveat that between the milestone/RC builds there typically won't be an upgrade.bat/sh script)
The main thing with upgrades between interim versions (or upgrades in general) is to make sure to back up your data prior to the upgrade - just in case.
Thanks,
Dan