Kayako will use your default email address to send any messages generated by either the notification center or automation you've built. The article details the process of updating the default address.
You can change your default email address from the admin area by clicking on Email in the sidebar. Hover over the address you want to switch to, and then click the Make default option that appears:
NOTE: When conversations are created through a specific Email channel, once you go to that conversation in Kayako, the predefined channel to reply to that conversation will be that same Email channel. This is so your customers will not receive a new email thread when you respond to them, and to keep the same recipient when they get back to you. You may switch to another channel at any time to send responses if you prefer.