Yes, you would need to register the replacement product you receive from the step-up program.

When registering the replacement product you would enter the place of purchase as EVGA (Step-up) and the date of purchase would be the date you received the stepped up product.

VERY IMPORTANT NOTE:

A stepup is effectively a new purchase.  And the warranty is treated accordingly, if it is not registered within 30 days, you will only have a one year warranty, same as any other product.