Thonny and Micropython run great together.
Here is a link where you can download different firmware.
You should also flash the firmware via Thonny. It is very simple. https://github.com/russhughes/ili9342c_mpy
I think I have the same problem, still trying to figure it out. I'm trying to gradually move an image in a loop by setting x / y and waiting, but the screen doesn't seem to update. Looking at your example I'm not sure how to apply a similar solution?