I have the exact same board. Yes, I had a hard time to get the IDE debugging working, but works just fine. Debugging only works via the native USB port, the right one in your first picture.
What eventually worked for me was installing libusbk for interface 2 using zadig. Interface 0 was left as WinUSB.
I cannot find the site/page where I found the correct instruction - there is a lot of bad info on the web.
EDIT 1: If you want to use the onboard RGB NeoPixel you need to bridge the RGB solder tabs (I soldered a zero Ohm resistor to it - it connects to pin 48).
EDIT 2: Found the page. It is for the Dice Device but is eventually the same. Check it here.