I thought I would post the solution to my problem of not being able to access my O365 WAAD through manage.windowsazure.com in case anyone else has run into this. In my case Technical support was unable to assist as I do not have a support subscription to WindowsAzure and Billing support (which Technical support said I should contact as they could link the accounts and correct the issue) said they could do nothing.
I think the problem stems from the fact that we were a Live@edu client which upgraded to O365. I have an organizational account and also a Live ID now. Even though I signed in to manage.windowsazure.com choosing the organizational login option, it appears that any accounts logging in this way that were created pre-O365 upgrade are appearing to manage.windowsazure.com as Live IDs. I verified this with multiple O365 accounts that were created in Live@edu. Of course, a Live ID does not have rights to my O365/WAAD environment and so I am not given the opportunity to see my WAAD.
The solution is to log into manage.windowsazure.com with an Office 365/Organizational account that did not exist in Live@edu (such as the firstname.lastname@example.org account that is automatically created). Logging in with this account properly (automatically) shows my Office365 WAAD. I then add my desired Live ID to my O365 WAAD and give it admin rights. WAAD lets you add Live IDs to your directory. I then have two accounts, an Organizational and a Live ID, listed in my WAAD directory.
I can then log out as email@example.com and log back in with my own personal Organizational Account (which is seen as a Live ID for whatever reason) and will then see my trial WAAD (created with the account sign-up process) AND my O365 WAAD!. After the trial ends, I receive a warning that I have no active subscription (the trial WAAD tenant is not visable which is fine) but I continue to see and be able to manage my O365 WAAD.