Hi,

1)
The documentation relates to the current release of all products. Atmel studio 6.2 and Arduino 1.0 are rather old now and it was too difficult/confusing for most users to maintain older documentation.

In 6.2 you need to right click the project name in the solution explorer and click View Properties. Or, with the project selected in the solution explorer press ALT+ENTER

2)
The rules for an Arduino project are that the folder name and the master .ino name must be the same. 

The additional rules for Visual Micro are that the atmel project name must also be the same ad the folder and .ino. 

NB: Atmel has a .ccpproj file name(s) and a solution explorer name.

An option is always to delete the visual micro/atmel studio project files and the __vm sub folder then reopen the .ino using "File>Open>Arduino project". Visual micro will recreate the project adding all files from the physical sketch/project folder to a new project.

3)
Finally keep in mind that Arduino compiles all files in the sketch folder. So leaving stray files in the sketch/project folder will be compiled regardless of their inclusion in the actual project. (This is all optional in the recent releases for Visual Studio 2015 (free) and not quite so recent Atmel Studio 7 version)