Not quite sure if I understand your problem, but let me comment anyway... A "route" is what you are needing, but sounds like you are not placing enough "waypoints" to get you there with out being confused by "line of sight". Unfortunatley, I think that that is how the GPS is designed to work. You either have to add to the amount of waypoints in your overall route, or have a GPS that actually shows you real time data overlayed onto your topo map (what I do) and then you can "see" what waypoint you are coming up to along your path. Many times there is a box where you select how many waypoints you want in your route, and/or the distance between them etc. Play around with this feature and see if it helps. But GPS reads like a birds flight, so following a convoluted path isn't really its forte.
I'm using a Magellan Triton 400, with Nat Geo Topo and I preload my map, trail, route, and waypoints all at once. I can see exactly where I am along the route, the path, or on the map depending on what I choose to highlight on my GPS functions. Then I can download any additional data when I get home from my trip as well. Hope this kinda helps...