Its sounds like your setup.exe is just a boot straper for an MSI package. You can create transform files to create an answer if this is the case.
Here is a link to a free tool from Wise, for some reason its not on the wise site anymore but its still posted here
http://209.104.132.210/InstallTailor_6_0.msi
I usually copy the MSI package to a staging folder and in that folder is an MST that is taliored for that machine. (I create one for each server that I need to install on.)
Look at the command line options for msiexe.exe
Otherwise looking to setup.exe switches there is one option that creates an SS.INI files that is also an anser file for older non-MSI packages.
Hope that helps.