I am assuming that you have grabbed the Alfresco Tomcat bundle (the community version). I am also assuming that you are running Debian Etch or beyond (if you are running experimental and things dont work, thats your mess to sort out).
Read it here
Yesterday I blogged about how to perform the most basic possible installation of Alfresco on a Debian system. That setup included using Hypersonic SQL as the database backend. Eventually you will want to migrate to using MySQL instead. Let us look at how to set it up.