Payara are the sponsors of the open source Payara Micro project, which implements the Eclipse MicroProfile specification. Payara Server is based on the open source application server, GlassFish. Payara Micro is based on Payara Server, albeit a slimmed-down version of it. As their website describes, Payara Micro is the microservices-ready version of Payara Server.
The way Payara Micro works is that a Payara Micro instance starts and then your MicroProfile microservice is deployed to it as a WAR file. For example, to start a Payara Micro instance, you would enter the following command:
$ java -jar payara-micro.jar
To start a Payara Micro instance and deploy your application to it, you would enter the following command:
$ java -jar ...