You can create templates for an autoresponse email to a ticket. The template is created via the ticketing system's rules, so you can create different templates for different conditions (as per the source email, the ticket title
You can also define different outgoing e-mail settings to different knowledge bases.
1. Go to: Setting--> Ticketing--> Rules
2. Under: "when
3. Define the relevant conditions per e-mail
4. Choose the action: "Send email" and click on "Edit email"
You will see this
5. Define the template and save it.