I'm not an Affinity Design user, however this answer would work for any vector image editor. They all work using the same basic principles.
There's no need to redraw anything. You could simply use the Pen Tool again to complete the paths to make fillable closed paths - shapes which overlap the circle.
Then remove the stroke, and set the fill to the same ...
You can adjust the stroke width as small as you like. Then expand the stroke. Apply Layer > Expand Stroke. It makes the curve a filled area which looks the same as the curve.
Boolean divide the circle below with the expanded stroke. Recolor the slice or move it away. Remove the tails of the divider.
Technically this doesn't fulfill the title of the ...
Here are two options for you.
Inkscape's connector tool is most useful if you want to constantly tweak the layout. It's a little bit buggy but normally yields handsome results. This tool doesn't work well with snapping enabled.
For more intricate designs use the node tool with snapping.