They seem to function the same. Manage is even "control in action or use" according to http://dictionary.reference.com/browse/manage. Control is a verb so isn't that in action as well? Thus, is it the same? I don't see them being listed as synonyms. If they are different, can anyone point out how they are different? This is driving me nuts.
It is here used in this context: "You will have the capability to control the system." Compared to "You will have the capability to manage the system."