Typically you would want your setup.exe to stay the same name every time you build. Especially the MSI filename. The version of the file can be set on the command line.
So for our setup, we specify the desired name of the setup.exe and msi filename in the product/release configuration of the ISM. Then on the command line, we always call the ISM with the same command line, which gives us repeatability/reliability.
"C:\Program Files (x86)\InstallShield\2012Spring SAB\System\IsCmdBld.exe" -p "E:\Path\to\the.ism" -y 3.6.356.2 -a "PRODUCT_CONFIGURATION" -o "E:\local\mergemodules"
-y sets the version (ProductVersion) which also sets the resulting EXE version
-a specifies the product configuration
-o specifies a folder for merge modules (we limit the merge modules we consume)