The user database is configured in the 'conf/server.xml' file.

Read the configurtion manual.... but quickly...

This defines the database file:

<Resource name="UserDatabase" auth="Container"
              type="org.apache.catalina.UserDatabase"
       description="User database that can be updated and saved">
    </Resource>
    <ResourceParams name="UserDatabase">
      <parameter>
        <name>factory</name>
        <value>org.apache.catalina.users.MemoryUserDatabaseFactory</value>
      </parameter>
      <parameter>
        <name>pathname</name>
        <value>conf/tomcat-users.xml</value>
      </parameter>
    </ResourceParams>

The 'Realm' element declares what database should be used:

<Realm className="org.apache.catalina.realm.UserDatabaseRealm"
                 debug="0" resourceName="UserDatabase"/>

If you want encrypted passwords (e.g. MD5), add a digest attribute:

<Realm className="org.apache.catalina.realm.UserDatabaseRealm"
                 debug="0" resourceName="UserDatabase" digest="MD5"/>

Other 'Realm' elements let you use other "back-ends":

<Realm  className="org.apache.catalina.realm.JDBCRealm" debug="99"
             driverName="org.gjt.mm.mysql.Driver"
          connectionURL="jdbc:mysql://localhost/authority"
         connectionName="test" connectionPassword="test"
              userTable="users" userNameCol="user_name" userCredCol="user_pass"
          userRoleTable="user_roles" roleNameCol="role_name" />