@Be.St.'s aprroach is true, but incomplete. I'm just copying his explanation with correcting the incorrect part.
IIS express configuration is managed by applicationhost.config.
You can find it in
Users\<username>\Documents\IISExpress\config folder.
Inside you can find the sites section that hold a section for each IIS Express configured site.
Add (or modify) a site section like this:
<site name="WebSiteWithVirtualDirectory" id="20">
<application path="/" applicationPool="Clr4IntegratedAppPool">
<virtualDirectory path="/" physicalPath="c:\temp\website1" />
<virtualDirectory path="/OffSiteStuff" physicalPath="d:\temp\SubFolderApp" />
</application>
<bindings>
<binding protocol="http" bindingInformation="*:1132:localhost" />
</bindings>
</site>
Instead of adding a new application block, you should just add a new virtualDirectory element to the application parent element.
Edit - Visual Studio 2015
If you're looking for the applicationHost.config file and you're using VS2015 you'll find it in:
[solution_directory]/.vs/config/applicationHost.config