Okay, I actually did something like that. I came across an article saying to run the below code to change the name of the default config file so it would activate last, which seems to have solved the first issue.
The second issue still eludes me. Registering a domain in the mapping tool doesn't seem to provide a redirect for other sub-domains of the same domain. e.g. If I register example.com that will work find but navigating to www.example.com navigates back to the base domain.