Maintenance updates for MQe are shipped as a complete new release.
Keep the install package for the current level, in case you want to restore it later.
After installation, check your classpath to ensure that the latest level of MQe is being invoked. If installing on Windows, make sure that you give the shortcuts folder for the new install a different name to the existing one.
For more general information on maintenance updates and their availability see the MQ family Web page at http://www.ibm.com/software/integration/mqfamily/.