Sorry, but I'm having trouble understanding your question. At 1:5000, given any reasonable line weight for the superhighways, side-by-side routes (like the 401 and 407 in Mississauga) should not touch each other. That would only start to be a problem around 1:30 000.
If you mean that the median is not falling in the center of the highway, that's usually solved by generating all the symbology (casing, color stroke, center stroke) from the same centerline file. At 1:5000, you may have different centerlines for westbound and eastbound lanes. On something like the 401 you may have additional centerlines for local and express lanes. If you don't wish to represent those as they come to you, you might have to perform some calculation to derive a new averaged centerline that you can then symbolize.