Hi George,
Thanks for the post. This is something a lot of folks run into.
You can do exactly what you want to do (reverse as you merge) using TopoFusion. You just need to dig into the right click menu. Once you add a segment to your merged track, right click anywhere on the map to get the menu to come up. You can then reverse the last segment added to match up the way you want. The key is to get the first segment you click on going the direction you want, then reverse any subsequent segments afterward, as you go.
Hope that helps, if it's not clear what I mean, don't hesitate to ask more questions!