Figured it out.
I know this is the Android forum, no need to flame me for mislocation. I performed this on my iPad, but the concept should be the same for Android.
So, I think that Wyse should make some of these options available in an advanced tab, instead of using the pocketcloud:// method to access a custom RDP file.
With that stated, I uploaded the custom .rdp file to an open location on my web server, added a link on the SBS portal with a prefix of pocketcloud:// (e.g. pocketcloud://www.mydomain.com/files/remtoeapp.rdp) and have users click on that link to use RemoteApp custom rdp config. I had to disable NLA on the server as I was only getting a black screen when connecting through PocketCloud Pro.
This is the contents of the .rdp file:
alternate shell:s:C:\Application Path\Application.exe
Lastly, unless you have your rdp externally facing, this would require a VPN connection on the tablet prior to accessing the custom rdp.
***EDIT*** the Smiley is a : and a D together... stupid emoticons.