Use File | Preferences | Map colours
Click on the coloured box to change the color, then click Apply or OK. If you want to save your colour scheme, you will need to "export" the colour file so it appears in your drop down colour schemes. The colours you want to change are Runway Background and/or Runway Extension.
The VOR's and waypoints from Bones site will not work, as RadarBox has it's own database of nav aides. All the outlines for airspace and airfields will work OK though.
Take a look at the manual (page 57 - Map Colors), this is covered in detail.