Assuming you are running the weavedinstaller on a Raspberry Pi, you add an SSH connection and then you add a VNC connection. One thing to be highly aware of is that VNC only became pre-installed on Raspbian recently and you may have to install a VNC server yourself if using an earlier version of the OS. I believe that support for RealVNC was added in the recent Raspbian Jessie images, but you have to enable it using raspi-config.
The weavedinstaller assumes a default port of 5901 - which is correct if you are using tightvncserver. I'm fairly sure that the default for RealVNC is 5900. Weavedinstaller doesn't "detect" the ports, other than to show a warning if you configure the weavedconnectd daemon to use a port for which there is no active listener.
Also see: http://forum.weaved.com/t/support-tech-notes/727