I think you may want to look at the parameters of MSIEXEC..
http://msdn.microsoft.com/en-us/library/aa367988.aspx

More specifically with the TRANSFORMS component ( the /t for the MST files): http://documentation.installshield.com/robo/projects/installshieldxhelplib/IHelpCmdLineMSI.htm

Here are some great articles here:
http://www.appdeploy.com/

HTH,

Kent
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