1. Do I have to restart JIRA when I change a template?

No. It is not necessary to restart JIRA when you change the TemplateMe! configuration.

2. Can TemplateMe! modify the default JIRA templates?

No. You can only edit the templates that you have created with this add-on. 

3. Are templates stored in JIRA's database? I mean, If I upgrade JIRA do I lose the templates or I keep them?

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.

4. Is TemplateMe! compatible with JSD Projects?

No at all. TemplateMe! is compatible with JSD Projects notifications. However, all the customer portal notifications won't be overriden.