Use the following command to copy your key to your Amazon EC2 instance. /you/.ssh/id_rsa.pub is the location to your ssh key, pem_file.pem is the .pem file you normally use to login, and user@ec2-instance.com is the user and hostname to your EC2 instance:
cat /you/.ssh/id_rsa.pub | ssh -i pem_file.pem user@ec2-instance.com "cat >> .ssh/authorized_keys"
https://mikeeverhart.net/2013/05/adding-an-ssh-key-to-amazon-ec2/
A command to open up an SSH tunnel at a given port (port = 9000 below):
SSH && ssh -i pem_file.pem -N -M -S /tmp/ssh_tunnel_%h.sock -L 9000:<rds-endpoint>:3306 user@ec2-instance.com -v