In a Payara server, the server's certificates are stored in the keystores file. There are two types of keystores used by Payara: Java Keystore (JKS), and PKCS12 (P12).

The JKS format is generally inferior to the PKCS12 format because it can only be used on platforms that support Java, and is less secure, and is less convenient to work with. However, the PKCS12 format can only be used in Payara version 6 or newer, whilst in Payara versions 5 or older only the JKS format can be used.

Therefore, in Payara server verision 6 or newer it is recommended to go with the "Using a New PKCS12 Keystore (P12)" section, but you can still use JKS if needed or preferred. In Payara server version 5 or older you must use the "Using an Existing Java Keystore (JKS)" section.