If you want to load all of the waypoints for a route, then the only way is to enter them all manually into mapsource. For the points where Chris doesn't list co-ordinates, then they are not important - he just gives some information and the km point along the route.
It would take an extremely long time to do this for all the routes, i'm pretty sure Chris would say this is not necessary - although, i'm sure many people have done so.
The downloads he gives on his site are for the 'key' waypoints only - ie: if you have these loaded they are all you really need and will be enough to stop you going too far wrong.
Morocco Overland ~ Routes
When you click on an area (eg: Morocco East) you get a list of the 'key waypoint files (.gpx)
When you download them they appear (on my pc anyway) as an unrecognised file type.
All you need to do is double click the file and tell the pc you want to select the type of program from a list, then just select Mapsource from the list that appears and 'robert's your mothers brother!!'
It doesn't matter where on the hard drive the file is when you do this.
Hope this helps