We are using InnoSetup to generate the installer of Substance Designer.
The whole set of parameters that can be used with the installer is available here : http://www.jrsoftware.org/ishelp/index.php?topic=setupcmdline 

You should put the license file in the following folder by default: ProgramData/Allegorithmic/Substance Designer/license.key

You can change this location with the following environment variable: SUBSTANCE_DESIGNER_LICENSE

Installing in Silent Mode (Via Command Line)

The flag to use to perform a silent install is "/SILENT". You can also use the "/NCRC" flag to skip the CRC (verification) of the package.

Example :

SubstancePainter_Installer.exe /NCRC /SILENT /DIR="C:\Installation\Folder\"