Ok, this is realy odd, how KiCad dosen’t understad two polygons on the same layer with different net names. I know I could use Cut-out, but hen i cant trace other polygon in that area. I’m talking about this situation:
I had the same issue some time ago but this is fixed in the newer versions.
You can (e.g.) just create a GND copper fill that covers the complete PCB. Set its “Priority Level” to “0”.
Then just create a new polygon with another net on top of the GND-polygon and set the “Priority Level” of the new polygon to a value higher then “0”. This will give KiCAD the information how the different copper-fill-polygons are stacked and in which order they need to be handled / painted.
You need to have a track ending in the polygon or a via with the corresponding net placed in there so that the polygone gets filled (otherwise it will not be filled - this took some time for me to find out)