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When setting up your private subnets. Ensure there is a local route for the cidr range for the subnets you wish to connect or for the whole VPC which is usual practice.
Your public subnets will have a different route than the private subnets because the default route 0.0.0.0/0 will have a different path. Other than that the VPC cidr range route is set as local and they can all route to each other.
You can use the DNS endpoint name of your RDS for your EC2 to connect to your RDS.
You will need to allow in the inbound rule the SQL port on the RDS security group the EC2 security group or CIDR as the source.
Not sure what you mean use phpadmin. Are you referring to a SQL tool like workbench? Where will this be hosted?
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