Hi Scott4077,
What do you mean by saying “SkyDrive account with my company email address”?
If it means you have already added your custom domain to Windows Live service (https://domains.live.com/), your custom domain couldn’t be added to Office 365 unless you remove it from Windows Live firstly. This is because a custom domain should be associated with only one Microsoft online service.
If it means you just associate your company email address with a SkyDrive account (from https://signup.live.com/signup.aspx?lic=1) instead of adding your custom domain to Windows Live service, you can take David’s suggestion. You can set up your company domain associated with Office 365 services. It won’t impact on your SkyDrive account.
Thanks,
Maggie Li