TWE has possibility to silently install via twe-x.y-z.exe file. To do that, rename the twe-x.y-z.silent.properties.txt file comming with TWE distribution into twe-x.y-z.silent.properties, put it into the same folder with the twe-x.y-z.exe, and normally start the installation. During the installation, there will be no dialogs asking you to chose Java, place to install, etc. This information is taken from twe-x.y-z.silent.properties file. Here is the content of that file, with the properties you should modify to customize your installation:
# Where to install Together Workflow Editor (default value is C:\Program Files\twe-x.y-z) inst.dir=C:\Program Files\twe-4.1-1 # Path to local java installation (obligated - has no default value) jdk.dir=C:\Program Files\Java\jdk1.6.0_24 # Startup menu name. (default value - Together Workflow Editor x.y-z) startup.menu.name=Together Workflow Editor 4.1-1 # Create quick launch icon (on/off) create.quick.launch.icon=on # Create start menu entry (on/off) create.start.menu.entry=on # Create desktop icon (on/off) create.desktop.icon=on