I used the plug-in to create an api and workspace. The Sencha folder is not included in the project by default.
In Solution Explorer, click on: "Show All Files"
Right+Click on "Sencha" folder and choose "Include in project"
Next, I right click on the ext folder where the sdk is, go to Add in Visual Studio Menu, and select Ext JS App. It adds an app. The bug is that all files get duplicated in Visual Studio. It's odd. On the file system, there is only one copy. But in Visual Studio, it sees two copies of each file, one it thinks is saved and the other not saved. To avoid this problem, I just create the app with Sencha Cmd in a command line and then in Visual Studio, i add the folder for the app to the project. That works.
I'm afraid to use the plug-in to add items since I fear it may duplicate files. So I just use Cmd along side Visual Studio.