You need to prepare the package first using the Adobe Enterprise Toolkit:
http://www.adobe.com/devnet-docs/acrobatetk/index.html
For other packages that don't have their own customisation tools you can use Orca:
http://support.microsoft.com/kb/255905
but you shouldn't edit msi files, create a Transform instead. But if you use Orca to look at the msi file, look at the Property table. Any Property expressed in Capitals can be passed to the msi as a Public Property. So if a Property name is SERIAL you could use the following command:
msiexec /i msiname.msi /qn SERIAL=12345-678910