I use Run Once pretty heavily, and yes I just use the actual commands that would be sent via the cmd prompt. I'm curious what command you are trying to run and what error it gives when failing.
Here is an example command I run to disable UAC and how it looks in Run Once:
REG ADD HKLM\Software\Microsoft\Windows\CurrentVersion\Policies\System /v EnableLUA /t REG_DWORD /d 0 /f
VCDX #104 (DCV, NV) ஃ WahlNetwork.com ஃ @ChrisWahl ஃ Author, Networking for VMware Administrators