From an AWS perspective the software charge and the underlying EC2 instance charge are separate. You can see in this image below the $0.622/hr charge is the software charge when running on a T2 Medium instance, but that the instance charge is a separate column $0.046 which is the On Demand pricing for the US East N. Virginia region.
When you purchase an RI for (in this example) a T2 Medium, AWS automatically discounts based on the inventory that matches. So if you had started the Cisco Marketplace item running on a T2 Medium and had purchased a T2 Medium RI that was not matched to any other existing instance, then you would see a discount for the compute automatically.
More details: How Reserved Instances Are Applied