First you need to setup the Cartridge Reader's jumpers like so.
The 29F016, 29F032 or 29F033 family of flashroms might come in a TSOP40 or TSOP48 package.
In case of the TSOP40 you need to align the flashrom so that there are 2 unused pins on each side at the top and 2 unused pins at each side the bottom inside of the ZIF socket.
For both cases plug the ZIF adapter into the most right position of the flashrom adapter since the TSOP48 variant follows the TSOP40 pinout and differs from your normal TSOP48 flashroms.
The two switches on the flash adapter do not matter in this case.
TSOP48:
TSOP40:
Now plug the flashrom adapter into the cart reader so that the 29F032 flashrom is facing towards you.
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.