If your server can be only accessed through a proxy server, you can add your proxy server settings into NETCONFc.

Select "Connect | Set Up SOCKS Proxy" from NETCONFc top menu bar:

Select Proxy type (SOCKS5 or SOCKS4),
Enter your proxy sever name or IP address, user name and password,
Click "Ok". 

Now you can connect to your NETCONF server via "Connect | Over SSH" or "Connect | Over TLS" as you would do normally.