Yes, this incremental building of routes (rubber-banding through your via points as you refine it) is the only way to fly with MapSource. I think a lot of folks never figure it out as it is fairly counter-intuitive to have to first click the route to select it, then click it again to stretch it. I would expect a dragging UI, although I think they do it the way they do so you can do other things like scroll and select other tools while in rubber-banding mode.
The issue of routing discrepencies between MapSource and the GPS has been a long-term bugaboo for Garmin. In addition to the GPS-varying mandatory-recalc problem discussed here, there is the issue that routing preferences are globals in both MapSource and the GPS, rather than "sticking" to routes. If these preferences were made properties of routes, they'd get transferred along with the route so you wouldn't have to manually make sure your preferences stay sync'ed. I suspect the reason for this problem is that Garmin never has standardized on a GPS-independent standard for routing preferences, so with 300-odd models in the field, trying to get everything the same would be an exercise in herding cats.