Waypoints are Saved as Favorites

Each has their place and use. MapSource waypoints will save to separate entries in Favorites. Those waypoints can be used to build a custom route using Mapsource. And they can be created and updated on the fly using the GPS while you're on the road.

Third-party software will almost always be aimed at creating Custom POI files. Custom POI files are harder to work with but can be more powerful because as you have seen you can organize them in ways that suit your needs.

So if I don't create Custom Routes, I'd have to manually select the next waypoint / destination.

Is there a way to combine all the waypoints to create a single route from A to B?

If you select your final Destination Waypoint and then select an intermediate Waypoint, it will ask you if you want to replace your current destination with this new selection, or to make it a Via Point. Select Via Point. You now have a 3-point route; Start, middle, and end. Many models only accept a single Via Point. A few will allow multiple Via Points.

Can you tell me where I can find the the TakItWithMe Program?

I used the basic GOOGLE search.
http://www.takitwithme.com/

Thank You Rayzers