If you create a template with the "All Service Desks" checkbox enabled, then when you activate this template it will be applied to all your help centers

All service desks option.

The remaining options relate to specific help centers and when activated, the templates will only be applied to them.

Particular service desk option.

Please note that this option has higher priority than the "All Service Desks" option!

That is, if you have the "All Service Desks" template activated and another template for a specific project, then the latter will be applied to the specific project.