Just keep in mind that people who are "cookied" for one domain will not be cookied for the second domain until they fill out a form on that domain (or click a link in a Marketo email that goes to a web page on that domain). From that moment on, they will be tracked on both domains.
Also, there is only one primary CNAME, the others are aliases. That CNAME will show be shown when you look at the landing page in the Marketo user interface. Also, if you drag images into emails or landing pages, those images will be hosted on the primary domain. You can manually change the URLs, but the CNAME will always be put in as default.