Hi Ann,
You can customize the ArcGIS Viewer for Flex application by simply editing some XML configuration files. This application has been designed with the "non-developer" in mind.
You can create your own Web mapping application from scratch using the ArcGIS API for Flex - this will require some developer skills.
I'm not 100% sure about the Emergency Management template, as I haven't personally used it. However, it looks like it is configurable (i.e., does not require programming) - but I guess it depends on whether or not it meets your business workflow requirements. I suggest you watch the video to learn more about the template.
Hope this helps,