You have three choices, with the current part you need to route the traces from the right of the RPI connector like this:
if that doesn’t do what you want (as in the case of trying to make a hat) then you either need to switch to this connector
Raspberry-Pi-Header-40pin-improved.fzpz
from this post
or to this new zero part which has that connector in it.
raspberry-pi-zero-oblong-pins.fzpz (25.0 KB)
to use either of the last two solutions you will need to change the grid size in pcb like this:
in order to be able to position a standard trace between the pins without colliding with a pin.
Peter