Doug,
Let us assume, you have the following in your script. The %MYVAR% variable is set to 0 and if you execute the script the Message Box displays 0.
Set Variable %MYVAR% to 0
Message Box "%MYVAR%" -- "Test"
But if you start your executable with the following command line, it will display "cool" instead of "0".
yourinstallername.exe /V MYVAR cool
The above sets %MYVAR% to cool (please do not add the %-sign around the variable name).
Does this help?