For now I'm using 8 and the documentation seems to be equally confusing on this. I want Odoo to identify who is writing out the response and who its going coming in for. But I can't seem to do this as it all goes through one email address with one user (the one which I set up the incoming/outgoing mail servers as).

Depends which version 8 and 9 are a little different. The docs for vers 9 are a little incomplete but quite useful ie https://www.odoo.com/documentation/user/crm/leads/generate/emails.html