Caleb,
I have Scripts and Config folders and an empty Log folder that I copy into the UD folder. Scripts has a separate ps1 for the endpoints of each dynamic page and a script defining the dashboard. Config has my nav bar logo image, a credential file my app uses plus any files that need to be copied into the UD structure: Dashboard.ps1, web.config, Index.html, favicon.ico, and license.lic. Dashboard.ps1 (posted above) is just a wrapper for launching the dashboard defined by the script in the Scripts folder.
This makes development and deployment easier, but should not impact behavior. I would expect -Design to work for you.
Thanks,
Tim Curwick