The top botton, 'organize my data' allows a user to create an new database or open an existing one. When a database is opened files can simply be dragged from the windows explorer to the menu after which they will be added to the database. Be sure to save the database before you leave this menu. More detailed information on indexing data can be found in the 'indexing data' section.
The next button opens the network window. Here you can start and stop the network server. The menu has the same options for opening and closing database files as the indexing menu described above. This allows you to keep multiple databases for different uses. When closing this menu, the network is automatically shut down. Due to some network management done in the background it may take a while before the network is shut down, and therefore before the menu closes.
For debugging purposes all modules send human readable messages to the main applications. These can be viewed in a separate menu by selecting the 'show messages' button. In many cases this information will not be of interest to the user and therefore the button can be left unset. If you are experiencing problems or want to follow what's going on in the background this is an essential tool.
Finally, the settings dialog allows you to alter atomsnet's configuration. Be careful, however, in most cases these settings are correct and don't need to be altered.