Hi Chris,

I think there is a bit of confusion here. ATE is a different product to Visual Micro. 

Visual Micro is a plugin and all that is required to setup is setting the location of the Arduino Ide in the Visual Micro ide locations dialog accessed via the tool bar apps list><Configuration Manager> or via tools>options>visual micro>application locations. You should also have been prompted when Visual Micro the first time Visual Micro was run in the Atmel Ide.

You can also optionally set a sketchbook folder but the default is whatever sketchbook folder is specified for the Arduino Ide.

After setting the location of the Arduino Ide you can cause Visual Micro to create an Atmel project simply by trying to open an existing sketch. You can do this a variety of ways but until you get to know the tool just use File>Open>Sketch project or File>New>Sketch project.

When you have a sketch open all of the standard Atmel build and debug/start options will compile and/or upload based upon the Arduino board and serial port you have selected from the tool bars that Visual Micro creates.

Visual Micro automatically finds the libraries and tools and is aware of the different versions of Arduino libraries based upon the current selected Arduino Ide (select from the tool bar). Visual Micro also uses the configuration files of the selected Arduino Ide so the boards list, programmers, libs, platforms etc. will be identical to those provided by the Arduino Ide. The option lists will also include any custom Arduino libraries and hardware defined for the Arduino Ide using the standard rules published on Arduino.cc. Changes and additions of new libraries and boards are automatically detected when you start Atmel Studio or when you click "Tools>Visual Micro>Reload Tool chains".

If you want to upload using a programmer instead of usb then tick "Tools>Visual Micro>Upload using programmer" and make sure you have selected a programmer from the programmers menu immediately above.

Visual Micro uses standard Atmel Studio projects for either avr or sam and simply detects when the project contains Arduino files and then overrides the standard Atmel Studio intellisense, build and upload processes. 

Aside from hardware and library compatibility (especially for the new formats of arduino 1.5.x) another benefit of overriding the build process to match how the Arduino Ide works is that it allows us to compile an Arduino sketch that contains multiple .ino sources whilst also providing us with double click drill down into compiler errors (nb: the Arduino Ide doesn't do that bit).

So we don't use .bat files, we don't use the external tools. We use the instructions defined within the Arduino Ide configuration files to compile and upload. In the case of avr chips the upload will use avrdude but the only way you would know that is if you switch on tools>options>visual micro>compiler>verbose.

Because you have used a different mechanism to create an Atmel Studio project for Arduino in the past it might be that Visual Micro doesn't recognize the project as avr or sam. We have not tested this combination. If you have problems I would suggest removing the .ccpproj from the sketch folder and any other sub folders. So you have a clean sketch, then open the sketch with Visual Micro and let it create a new project. 

Here are a few articles from the visual micro wiki, the instructions are the same for both atmel studio and visual studio

http://www.visualmicro.com/post/2011/10/04/How-to-test-a-new-installation-of-Ard...
http://www.visualmicro.com/page/How-to-compile-and-upload-to-an-Arduino-using-Vi...
http://www.visualmicro.com/post/2011/10/27/How-to-add-an-Arduino-library-using-V...

Great, thanks for letting me know.

Better documentation is the next job on the list!