I'm guessing you want Tomcat to create connection pool to MySQL database. In that case, you don't need to configure server.xml file. In the context.xml file you need to add a <Resource>
element, something like this:
<Resource name="jdbc/MySQLPool" auth="Container" type="javax.sql.DataSource"
factory="org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory"
maxActive="100" maxIdle="30" maxWait="10000"
username="USERNAME" password="PASSWORD"
driverClassName="com.mysql.jdbc.jdbc2.optional.MysqlConnectionPoolDataSource"
url="jdbc:mysql://localhost:3306/test?useUnicode=true&characterEncoding=Cp1251"
removeAbandoned="true" />
(I'm not sure if that's the correct driverClassName for MySQL, but your Resource should look somewhat like this).
For more info, try checking Tomcat's documentation on JNDI Resources and JDBC DataSources.