Found the solution. Note: this works with VS 2010 too.
Run your projects (Start Debugging in VS 2012). This will show up the two command prompts.
For each command prompt
- Position the command prompt on your secondary screen
- Open command prompt window > Properties > Layout
- In the "Windows Position" group box section, uncheck "Let system position window" (see attached image)
- Click OK and then close the command prompt
Next time you run your projects, your windows will be positioned to the location you set them to.