Welcome to the forum, Mick.
I think I understand your problem, but perhaps not. I found that S&T plotted the route according to your stated preferences above just by starting at Trancas Street in Napa and ending at the Getty without adding any stops or waypoints. Whatever you do, though, I would not fully trust any navigation program to just get it right automatically; I think you should follow the projected route on the map and in the driving directions to assure that it is going the way you want.
If you did want to insert your own waypoints in the form of road names or numbers S&T can sub-optimize. For instance, if you do a search for "I-80" and add that to the route, S&T will pick some unhelpful point on I-80 half-way to Reno. Therefore, you don't want to do that. I would rather start with the route start and end points only and then just drag the route to the highways you prefer. To avoid having waypoints where you don't want them as you describe, just click on them and move them to where you want. Certainly, if a waypoint is off the road, drag it back on. Also, I find dragging the waypoint to the end of a road segment (just before the next turn off the road segment it is on) will give you the cleanest directions.