Here's some advice if you initially installed your Kentico app and now want to decouple it, such that you can use separate logins in your application and the cms desk. This assumes you initially installed with the helper app, and have the source code version.

1. Create a directory to use as the application root for the new CMSDesk app.
2. Configure an IIS Application as /yoursite/cmsdesk based on the directory above.
3. Copy the CMSDesk_cs folder from the Kentico source to the directory you configured above.
4. Copy the files in the /cmsdesk/metadata directory of your original app into the meta direcotry of the new cmsdesk app
5. Copy any custom icons from the /cmsdesk/design/icons directory into the new one.
6. Update the web.config properties in the new cmsdesk application by copying the values from the old app
7. Rename or move the cmsdesk subdirectory from your original project.
8. Comment out the Kentico generated code in the Global.asax.cs file:
- Application_AuthorizeRequest
- Session_Start (but leave the preffered culture section)
- There may be other references that I deleted instead of commenting out, basically anything dealing with users will no longer be needed
9. You may remove the code dealing with authorization and user id's from the Functions file if you wish.

So far I've had good luck with it running in this mode, hope this helps someone. There's most likely a few details I've omitted.