Can you post your connection settings, it will be much easier for all of your to help you configure the connection. Also please search through the forums. You should be able to see a lot of hits on how to configure your JDBC connection.
MS SQL 2000 drivers jar files (msbase.jar, mssqlserver.jar, msutil.jar) should be in \webMethods6\IntegrationServer\packages\WmJDBCAdapter\code\jars and webMethods6\IntegrationServer\lib\jars