The Skype integration module uses an API, which Skype exposes to build up a Windows service that acts as a proxy for chats. The service itself exposes an API that handles chats, keeps track of ongoing chats, the status of Skype users, etc.
The template package uses this functionality to build up chat functionality in EPiServer. The chat functionality works so that one or several Skype users are registered as "chat owners". Chat links are added to EPiServer pages, so that when visitors click the chat link, the chat message is redirected to any of the "chat owners" (if they are online).
It is also possible to add notification functionality to a page so that you receive a Skype notification when someone requests a particular page. You can then also choose to enable chat, which results in the user receiving a pop-up dialog, where he/she can start to chat.
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