Reserved Instance cost savings automatically get applied to an on-demand instance that matches the:
- instance type
- Availability Zone
..of the Reserved Instance that you have purchased. So, assuming you have access to your AWS Console, you can go in there, search for and purchase a Reserved Instance that matches the above specs of your on-demand EC2 ArcGIS Server instance, and that Reserved Instance will get applied to the matching on-demand instance. Now, that said, I have never used CloudBuilder, but I am assuming all it does is design and possibly deploy an AMI for you, which should then be available to you in your list of EC2 instances in the AWS Console. The docs on Reserved Instances are pretty thorough, I suggest you read through them at length before making your purchase.