When creating a new virtual desktop on the server host, the NoMachine server starts the default desktop as set on the system.
If you want to run a different window manager/DE, you can choose to run a custom session (click the link ‘New virtual desktop or custom session’) and specifying the WM to run in ‘Run the following command’ in the successive panel.
Alternatively, you can set it on the server by editing the configuration files. The following articles provide more information about this:
Desktops environments supported by NoMachine 4 – http://www.nomachine.com/AR10K00725
How to run a desktop environment on Linux different from the default one with NoMachine 4 – https://www.nomachine.com/AR04K00667