I've been going through this a bit too. I had it working fine in for GW 14.2.0, but had a fight with it today trying to update to 14.2.1. Here's what I've had to do so far, but please let me know if you get the msi to work properly...
1. Put the client directory from the full download in your Repository.
2. Edit the setup.cfg file and add it to the client\win32 directory.
3. The first steps in my package are a message to my users and a command step that stops the GW processes. Just using: %SYSTEMROOT%\System32\taskkill.exe /f /im grpwise.exe /im notify.exe
4. Do an Install step and point it to the "install.bat" file they have in the win32 directory. They actually have it set up so that it installs the required prerequisite C++ redistributable packages and the client.
5. Make sure that you set "/silent" as your parameter for that .bat file.
6. Include the Entire Directory! Check the box!
7. Test it on a machine you control!! Every time they update it something goes wonky. With the 14.2.1 update, the bat file left out a line that called the parameter for the 64bit version of the 2013 C++ redistributable package so it just hung. Took me a while to figure out which part was hanging, but its up and running now.
The only other way I've found to do it is to do an Install step for every C++ file, each with it's own silent parameters (and they're different some years), then a step to install the "wse3.msi", and finally a step to install the "groupwise.msi". Again, the GroupWise MSI file REQUIRES the entire directory, so you have to copy 500MB of data for every install. :/
The second way's not bad, I'm just being lazy and didn't want to update it every time they added in another C++ component... LOL.