How do I enable dirsync on a Office 365 domain thats currently in use?
Or in other words, I have a Windows Azure Active Directory domain that is associated to my Azure account. When I run the Azure dirsync tool, directory integration says dirsync has never run, even though I can get dirsync to run on test domains (with SSO enabled).
How do I convert this WAAD domain, without SSO, and currently in use with O365, so I can authenticate with ADFS?
How users are created in your directory and how they sign in are two different (although related) subjects.
DirSync itself only copies from your on-premises AD to your Azure Active Directory (which is the user directory Office 365 is based on). You should be able to do this with an existing domain by following the Directory synchronization roadmap.
If you want to set up federation so that users can sign in using your on-premises AD FS, this is commonly done after setting up DirSync, but doesn't actually have to happen in that order. (In fact, if you create the users manually in AAD, you don't technically have to set up DirSync).
Since you mention the domain exists, you are probably interested in the "Convert a domain" section of Set up a trust between AD FS and Windows Azure AD, which shows you how to hand off authentication (sign on) to your AD FS. Summary: run the following on the machine that has AD FS:
Convert-MsolDomainToFederated –DomainName <domain>
