I think you are looking at the wrong section of the GUI.
The latest SW versions of the gertbot (from 2.5 upwards) supports quadrature encoders natively.
If you have connected the quadrature encoder as per the manual you can interface with it using the Gertbot GUI.
In the GUI switch the motor to DC/brushed, then using "more" click till you get a section about Quadrature encoder.
Tick the box next to "Quadrature encoder on".
You can then use the "position" and "SET" to set a value to the current position.
To read the quadrature encoder current value press the 'read' button.
You can press the button also whilst the motor is running.
With the quadrature encoder enabled you can give 'go-to' commands to make the motors run until the 'goto' value
of the encoder is reached.
Having said all that: I notices a big omission in the manual: How to connect quadrature encoders is not mentioned anywhere!!
You connect them to the end-stop pins (Thus you can use either end-stops or a quadrature encoder, but not both.)
I am banging out a new version of the manual as we speak.
You may need to upload the latest SW to your gertbot board. For that there is an upload GUI: gb_upload.
(There is a Pi and a Windows version)
and the SW release 2.6 is here: https://www.gertbot.com/gbdownload/rmc/rmc_2.6.crypt