No. It is not necessary to restart JIRA when you change the TemplateMe! configuration.
No. You can only edit the templates that you have created with this add-on.
Yes. All TemplateMe! configuration details, including the actual templates are stored in JIRA's database. You will keep them during JIRA or add-on upgrades.
Yes, TemplateMe! is compatible with JSD Projects notifications. However, all the customer portal notifications won't be overriden.
Yes. Create a new empty template by clicking and then go to Tools > Source code in the template editor:
Then paste in the source code pop up screen your custom made template html and save the template.
You can use the following code to add any custom field to the issue: $!customfield_XXXXX where XXXXX is the id of the custom field. For example: $!customfield_10100