So you want to use your own domain names with Atlassian cloud apps (jira, confluence, …)?
The short answer: Currently, you can not do it.
Atlassian cloud apps are served from the domains from *.atlassian.net (for any OnDemand/Cloud Customers) *.jira.com (for legacy Studio customers; no longer available).
This is a very big limitation for the Atlassian cloud apps. It is big SEO and marketing issue. It does not show as much professionalism to your customers and your users get confused if they get redirected to some other domain in order to view your manual. Furthermore, Search engines will not credit your hard work on the manual to your domain.
However, Atlassian for its reasons do not think that this is a limitation . It seem that this business decision and not a technical decision – Today, It is common that hosted services and SAAS-like environments to offer custom domains via custom CNAME.