Reserved instances are a billing feature, not a technical feature.
You can purchase a reserved instance and the discounted hourly rate will apply to already-running instances, without needing to do anything to them.
Just make sure the reserved instances you purchase are:
- in the same availability zone as your already-running instances
- of the same instance type (m1.small, c1.medium, etc) as your already-running instances.
As soon as the reservation cost clears your credit card you will see the discounted hourly rate take effect for your already-running instances.
Amazon's docs could be a lot clearer on this.
http://aws.amazon.com/ec2/reserved-instances/#4