To connect to SSH on your EC2 instance using a remote.it proxy connection through the remote.it web portal, start by clicking on the new Device Name to open the Services Dialog.
Now click on the ssh service you created.
This gives you parameters you can use for an AWS command line using your PEM key over a remote.it connection.
Use the values above in the following ssh command to connect to your AWS instance over remote.it:
ssh - i <local PEM key> <user>@<Host Name> - p <Port>
This sounds like a job for the API!