Figured it out. Here's what I did:
Import-Module RemoteDesktopServices
cd RDS:
New-Item –Path RDS:\RemoteApp\RemoteAppPrograms –Name Workbook.xlsx –ApplicationPath "C:\Program Files\Microsoft Office\Office14\Excel.exe" –CommandLineSetting 2 -RequiredCommandLine "E:\ProcessingFolder\ClientName_Cube.xlsx"
This creates an entry that points to Excel but specifies the path to the workbook in the RequiredCommandLine parameter. The "2" setting for CommandLineSetting forces the Remote App to always use the supplied RequiredCommandLine parameter.