No, Cloudera Manager upgrades do not upgrade CDH at the same time. You can choose to upgrade CDH at a later time, or not to upgrade CDH at all, so long as the new version of Cloudera Manager supports that version of CDH (in your case, it does).

Please be sure to follow the upgrade instructions when doing the upgrade, as there's some special considerations for a major upgrade.
http://www.cloudera.com/content/www/en-us/documentation/enterprise/latest/topics/cm_ag_upgrading_cm....

I also highly recommend using the latest version of Cloudera Manager, which can support all versions of CDH4 and CDH5. Many bug fixes, new features, and improvements have come along in the one and a half years since 5.0.1 was released, including an improved CDH upgrade experience for when you choose to do that.