Hello.
We are not entirely familiar with the ESP8266 ESP-12E, but it seems like you would need to use DTR (output) and RTS (output) on the AVR programmer to control GPIO0 and EN, respectively, to automatically enter the bootloader before copying MicroPython onto the board according to this documentation on GitHub.
I did a quick Internet search and found several tutorials on programming an ESP8266 board with MicroPython. You might consider looking at some of those tutorials to get some idea of how to load MicroPython onto your board (if you haven’t already done so). If you have not done so already, you might also consider posting about your issue on the MicroPython forum, as it has a much larger community that focuses specifically on MicroPython.
- Amanda