Waypoints are a mixed blessing. I find them more plague than profit sometimes.
Question: How may waypoints (as opposed to viapoints) do you actually need on each route?
For instance, let's say you want a day's ride of three hundred miles, from one hotel A to another called B, via, a museum in town X and a viewpoint on road Y.
I would find all four points on the map. Then, using Route Tool, simply join them up manually in the correct order and save the route as: 'To B from A via X and Y" or "From Calais to Dijon, via museum and view'. The plotted route would then take me past the museum and the view point, without a doubt. I might then, create Favourites (which are only waypoints) in the route called:
Hotel A
Hotel B
Museum X
Viewpoint Y
The four locations will then appear in my favourites on the GPS device. So that if I went off route, or decided to miss out the museum, I could later simply click on either hotel B or viewpoint and the device will take me there.
ALTERNATIVE
Open Mapsource on your PC.
Click on Waypoint Tool
Click on wherever the points on the map you want to go to, in any order you like.
Little black flags will appear on the map. These are the Waypoints you are creating but they are not joined up by any route at all.
As you create them, they will also appear in the box on the left of the Mapsource screen, in exactly the order you pinned them onto the map. For instance:
Calais, Lyon, Paris, Bruxelles, Madrid, London. Unless you wanted to to the cities in that order, it would be a crazy route.
Now, in the box to the left, highlight all the cities, so they turn blue. Do this by left clicking on the first (Calais) - it turns blue. Now hold down the UP arrow key on the keyboard and left click on the last city, London. All the cites are now blue.
Now, right click in the middle of the blue box and select: 'Create route using selected waypoints'. Your PC will then join the wapoints up in the most logical order, using the Preferences you have set.
You can now change the order or drag the route around (using the Selection tool) as much as you like.
You don't even have to have all the cites in. You can just highlight, say four, of the cities by holding down Ctrl and left clicking. You PC will then create a route joining just these four cities up, leaving the two other cities as simple waypoints which will appear in your Favourites.
GOOD TIP 1:
Play with the thing, using say a map of the area around your house over 100 square miles. This is easier as you can imagine it and see what the programme is doing.
Play with cutting and pasting way points or chunks of routes into another route.
Muck around in Route Properties.
Change Preferences, to see what differences it makes.
Re-order them manually. Create folders, with several separate routes in.
Send routes and waypoints to the device. Turn it on and see what happens and how they appear.
You can't break it.
GOOD TIP 2:
Don't make single massive routes, involving days upon days of travel. Break them up into bite sized chunks. 400 miles is plenty.
GOOD TIP 3:
Keep playing with it. Suddenly it will all click into place.
GOOD TIP 4:
You really cannot break it.
GOOD TIP 5: It is so much easier creating routes, using Route Tool. It takes a bit longer but you, and not a dumd device, chooses exactly where you want to go. But, the same dumb device is very good at sorting masses of data.... so don't be too hard on it.
GOOD TIP 6:
Ignore all of the above if I have completely misunderstood your problem.