Oh btw: I know I can disable auto-routing for just the ground tracks, but then I usually can't find neat tracks for all the grounds.

Your project is private so only you can see it.

Without sight of your project the following comments may possibly be irrelevant but here they are anyway:

1. Reducing the number of ground and power connections can easily cause signal and/or power integrity problems.
2. Using only a single sided PCB can cause the same problems.
3. If you have your PCB made by EasyEDA it costs the same to have a double sided PCB as opposed to a single sided board.

For some background to this:

https://easyeda.com/andyfierman/Welcome_to_EasyEDA-31e1288f882e49e582699b8eb7fe9b1f

For reference see: https://cdn.sparkfun.com/assets/learn_tutorials/3/2/5/bplus-gpio.png

So for ground, I don't really care if it connects to pin 4, pin9, pin 20 or any of the other ground pins. However, I don't need any traces from pin 4 to pin 9, as these are already connected internally.

Sorry but your project is private so only you can see it.

Without sight of your project it is hard to make any meaningful comments based on the information you have given us so far.

i have exactly the same problem, it doesn't need to share a particular project, we all make a raspi HAT products, how to make some pins internally connected ?

@bigexxx,

Please do not assume that "we all make a raspi HAT products".

If you would like help on a particular issue, please be prepared to provide enough information from which others - who may be more knowledgeable about signal and power integrity or PCB layout but may be less so about Raspberry Pi HATs - may be able to offer useful suggestions.