I have a domain name for my forum (not the forumotion one) and would like that to be used as much as possible.

When there's a PM members get an email saying there is a new Private message including a link.

This link is the 'old' forumotion's address and not the proper domain name. Is there somewhere where I can change this setting?

Thanks in advance.

Why would you want to change this? You are representing forumotion by using the same domain, and I don't think that you can change this. You might change the URL, but you are still using forumotion and that is what will be displayed!