Are you referring to the Custom UI Admin guide for all of this? This stuff is in the guide, if you want a reference.
You don't need to restart the vApp when your changing these alerts - just restart the outbound alert handler, which you'd create to define the SMTP server.
Instead of starting from scratch, you can just duplicate a template and it's permissions for this test. Ensure you get the perms right on the template file.. admin owner, etc, otherwise it won't work. Look at the OOTB templates as a guide for perms.