Nomadesk 6.0.8 will be released on Tuesday, October 6th and will be fully compatible with OSX El Capitan.
If you want to use the current Nomadesk version, 6.0.6 you'll need to do the following in order to get it running under El Capitan:
1. close down Nomadesk
2. go to system preferences
3. in the OSXFuse options, choose uninstall
4. download OSXFuse from http://sourceforge.net/projects/osxfuse/files/osxfuse-2.8.1/osxfuse-2.8.1.dmg/download
5. run the OSFuse installer
6. during installation, be sure to check the MacFUSE compatibility layer option otherwise it will not work
7. restart Nomadesk
Should you still encounter any problems after those steps, please contact our support team.