Currently you would have to connect an ALM project and a JIRA project manually.

We have several thousand ALM projects (all are automatically created when a new project is started and based on the same template).
On the other hand, we will have automatically created JIRA projects too.

If we want to connect them in an efficient (automated) way we need to 

- create a standard sync template where all fields and ways to sync are included (harmonized over all projects)

- and then just apply the template to MF Connect to start the sync between both projects

without any human interaction (Maybe simply via API connectors).

Without such a possibility it is not possible to use it in a larger environment (We can´t do that manually and it has to be harmonized over all projects because of Audit and reporting issues).