Custom runtime settings are controlled in the “App → Settings” section of the App Explorer in Studio Pro. Once you’re in there, go to “Configuration tab → Choose a config and edit → Custom tab”. That’s where you put the settings from the link you found.
Now, if all you have is a PEM file, then you probably have a Certificate Authority cert. If that’s the case, you’ll use the CACertificates runtime setting with a path to your PEM file. That’s not really two-way SSL though.
For two-way SSL you should have a client certificate where you hold the public and private key. If that’s the case, you’ll have a .pfx or .p12 file, and you’d use the ClientCertificates, ClientCertificatePasswords, and related runtime settings.