Is there anyway I can use PHPStorm to sync with my EC2 box through SCP? EC2 requires a private key to connect to it. I don't see any option for SCP in the deployment configuration section
SCP is file transfer over SSH, a newer version of which is SFTP. Both just work over SSH, if your server is accessible over SSH then these are the options you have. You're simply looking for the SFTP mechanism in PHPStorm with Auth type of "Key pair".