I need to run queries against two tables in separate AWS RDS instances, and I wanted to setup linked servers. How would I do that with AWS RDS?
You don't. AWS RDS does not allow you to replicate outside of an RDS, not even to another RDS. If you need slaves or redundancy, you need to use the Read Replicas or Multi-AZ features of RDS, or you need to set up your own database infrastructure on standalone EC2 instances.