Hi Nathan,
Do you mean you would like to change the default domain to your custom domain?
If so, please refer to the steps below:
1. Login to Office 365 with an administrator account.
2. Click your company name on the left-hand navigation bar.
3. Click Edit in the pop-up window> Change Default domain to your custom domain in the drop-down list.
If my suggestion is not applicable to your situation, please feel free to post back with more detailed information and I will be glad to help you.
Thanks,
Kevin Huang