There's one Server.ini for each server account you create, stored in a folder that represents that server. For instance let's say you create an account called "Sputum News". The full path to this server will be:
/boot/home/PineappleData/news/Servers/Sputum News/
Inside that folder you'll find Server.ini, which contains all the data Pineapple News knows about your account. It is in the same format as PineappleNews.ini and it should similarly only be edited while Pineapple News is not running. There is very little reason to edit this file by hand however as almost all the data is editable from the main Pineapple News program window. To do so, right-click on the icon for the server you're interested in and select Properties.
The file contains only one section.
Hostname This is a string that is the DNS name of your news server, for example news.isp.net. If your news server doesn't have a DNS name you can put a dotted-quad IP address here.
Port This is the only field that can't be edited from the main program window. It is the TCP/IP port number on the news server computer where Pineapple News will attempt to make a connection to send and receive articles. The default is 119 and unless you know your news server is using a non-standard port number there is no reason to change it.
Timeout This is the amount of time Pineapple News will wait for a response from the server before declaring the connection dead and pulling the plug. The default is two minutes, specified like this: 2 minutes. You could also specify the string as a number of seconds, i.e., 30 seconds.
PostName This is the string value that is displayed in the headers view as "Author." It is required.
PostMail The e-mail address that will be added to the headers of your posts. Many people don't like to put their real e-mail address here for fear of receiving reams of spam.
PostOrg This is a string that will be added as a Organization header to your posts. It is not required and can be left blank.
Login A boolean value (Yes or No) that says whether or not your server is secure and requires a username and password to use.
Username, Password The login ID that will be used if the Login setting is Yes. Unfortunately the password is saved in the file as pure text. I haven't yet searched around for an encryption algorithm I can use.