Yes! NationBuilder has a concept of "broadcasters", which are the people who responsible for all your external communications. You connect an email address, Twitter and Facebook account to each broadcaster. When you send an email blast, you select which broadcaster it should come from, and the email address associated with that broadcaster is the one which is used. The same thing is true for each autoresponse - you just select which broadcaster you want to use from a dropdown menu.
For more on this, check out our how-to on setting up an email blast.