While it's possible to run a Delivery Recipient Report to confirm that an email message was sent to both the Primary and Secondary Email address on file for a constituent, there is no way to know which email was used when the constituent took action with the message. Interactions are recorded in Luminate Online by the Constituent ID. When both a primary and secondary email address are on one record, using one Constituent ID, it cannot be determined which email address was used. 

An alternative suggestion is to create a separate constituent record for the Secondary Email address on file and have it be the Primary Email address on the newly created record. In this way, each record would be using a different email address and the interactions would be recorded on the appropriate record to know which email is being used to interact with the message.