The concept behind the original PA55 is that users do not need to remember complex passwords but should be able to deterministically generate complex passwords from rather simple information that the user can remember. Specifically, for every complex password, the user needs to remember a master secret (common for all passwords) and a hint (specific to each password).
NYAPS – Not Yet Another Password Store – actually stores (of course, encrypted) something. Instead of storing complex passwords (like most password managers do), PA55 NYAPS stores information on how to generate the passwords. One could see it as storing the hint in PA55. These are called password generation settings or password settings or simply settings. Each such encrypted file can contain multiple settings for multiple passwords. However, the master secret is still not stored and is used to generate the complex passwords.
The settings stored include specifications of desired password length, an issue number (which helps with generating new passwords when the services require them refreshed periodically), and the choice of character sets. The user can now choose to include characters from brackets, digits, lowercase letters, special characters and uppercase letters.