Rooms
All the devices and scenes in Vera are grouped by rooms. So you must list the rooms in your house, and then on the devices page, you need to specify which rooms your devices are in. Some devices, like handheld controllers, may be used throughout the house. In this case, just pick the room where the device is most commonly used.
When you create a scene you must add the scene to a room as well. Note that what room you add a scene to does not have any effect on what devices it can control. For example, you can create a scene in the "Living Room" that turns on bedroom lights. Create the scene in whatever room you are most likely to want to use that scene. The reason for putting scenes in rooms is just to make it easier to keep track of which scene is which and to quickly find the scenes for the room you are in. For example, on the remote controls like iPhone and mobile phones, when you enter a room you need only pick the room you are in once. Then you will see all the scenes in that room without being distracted by all the other scenes in other rooms. This also means you can create multiple scenes with the same name in different rooms. For example, you may have 3 scenes called "go to bed" in 3 different bedrooms. Each scene will do something different. Some scenes are not really tied to a room, or are used throughout the home or in different rooms. For example, you may have a scene called "Entertaining Mode" which you use when guests arrive. You can put this scene in any room that will allow you to easily find it, remember the purpose of putting scenes in rooms is solely to make it easier for you to find the scenes. In a case like this, "Entertaining Mode" would probably be put in the "Entry Room" or "Living Room" if that's where you usually greet your guests.
For more advanced users, if you have a very large house, or if you want to create graphical floorplans to control the devices with icons, you can also create "Sections", and organize the rooms by section. Examples of sections may be: "First Floor" and "Second Floor", or "Main House", "Guest House" and "Grounds". Create sections by clicking the "Advanced" tab and choosing the sub-tab "Sections". You can create a floorplan for each section using your favorite paint or draw program and upload them to Vera on that page. You can also position the devices on the floorplan. Before you do this, go back to the Rooms tab and be sure to indicate which section each room is in. Since most users don't create sections, by default, Vera has only one section "My Home" and all rooms are put there.