I think it depends what you mean by "schedule it to run every hour"... NiFi itself would always be running and different processors can be scheduled to run according to their needs. Every processor supports timer based scheduling or cron based scheduling, so using either of those you can set a source processor to run every hour. You could also use the REST API to start and stop processors as needed, anything you can do in the UI can be done through the REST API.
For best practices for upgrading NiFi see this wiki page:
Deploying changes to production, there are a couple of approaches, one of them is based around templates:
Some people also just move the flow.xml.gz from one environment to another, but this assumes you have parametized everything that is different between environments.