Innovator right now does not offer the possibility to specify settings like port directly in the InnovatorServerConfig xml. There are tons of support requests for this feature, but I don´t think it´s really something Aras is working on.
Right now you have to specify all via IIS. You said you can successfully send emails already? Than your solution should be fine.
I faced the similar challenge, but weren´t able to solve emailing via IIS. It´s possible to use custom code for emailing. In my case I replaced parts of the Innovator emailing engine with a custom version that allowed me to email without changing anything in IIS and specify credentials in the server config file. But it´s not as elegant to use as the inbuilt email service.