First you need to setup the Cartridge Reader Shield's config switches like so.
Then insert the 29L3211 flashrom into the SOP44 ZIF socket, plug the ZIF socket into leftmost position of the 8bit flashrom adapter and finally plug the flashrom adapter into the cart reader.
You also have to adjust the two SMD switches both to the top position.
In the main menu first select "Flashrom Programmer" and then choose "8bit adapter".
To program the flashrom you need to erase it, then do the blankcheck and finally select write to flash it with your rom.
While writing a rom to the flashrom the led should blink constantly until the flashing process is completed.
And remember when you put a 29L3211 inside a SNES cart it will need a 104nf capacitor between GND and Output of the AMS1117 3.3V voltage regulator or else there will be read errors.