Just found this awesome extension that I was looking for:
With this extension you can right click on a web project in Visual Studio and associate a console project as a WebJob. After doing that when you publish the web project the webjob project will be published into the correct location in your Azure Web Site
http://visualstudiogallery.msdn.microsoft.com/f4824551-2660-4afa-aba1-1fcc1673c3d0