We are in the process of setting up additional microsites with different branding and different cname. My question is, now we want to send email from the other domain/cname in addition to our default. How/where would this be set?
First, your terminology is a bit off. You aren't creating "a different CNAME." The CNAME is the same: mkto-{{nnnn}}.com in the case of your email branding domains, {{accountstring}}.mktoweb.com in the case of your LP domains.
When you create a CNAME DNS record what you're doing is creating a new alias for the same CNAME. pages.example.net, pages.example2.org, pages.example3.info are aliases, not CNAMEs.
That aside, if you want to send from a new domain, add it in Admin » Email » SPF/DKIM. Unless you have the branded sender option set up for your instance, you don't need to worry about SPF, but you do need to worry about DKIM and set up the provided DKIM record in your DNS zone, just as you (hopefully) did for your original email domain.
I apologize: my tech team took care of that part of it. I actually figured this one out soon after posting--that I'm able to toggle within the email itself. (I couldn't delete my initial question.) Thanks for your help!