We are using Marketo for three separate business lines that are sharing leads, but we aren't using workspaces, so we have come across a few interesting challenges. Most recently we needed to figure out how to use the Track Links feature for each company. Initially we sent a test email from CompanyB via an admin account that had the email branding domain for CompanyA. That's when we noticed that the links were showing CompanyA's domain.
The fix for this is actually very simple. If you have your email CNAME setup for multiple domains you can use each of them as the default branding domain in a separate user account.
Since we have three domains I created a generic email address for each and added each as a new user with an admin role. In each account I went to the Email section under Admin and changed the default branding domain to correspond with that particular business line. In the Marketo Product Docs it states, "Every time you create a new email the default values you set will be used. The change is only applicable to you and not for other Marketo users."
The trick is that whichever account created the email, whether by cloning, using a template or coding from scratch, gets to own the links within it. So if you are in CompanyC's account and you clone an email created by CompanyA, the new email will now attribute all links to CompanyC.
Here's an easy way to remember how it works...
She who creates, dominates.