Just to follow-up. It turns out that WD SmartWare is smarter than I first thought: It backs up on a schedule I’ve set both for C:\ and D:\ partitions of the single drive. At first it appeared that only one or the other drive was chooseable from the drop-down menu but not both. However, it turns out that they are simply set up as different backup profiles with their own schedule. So one could set C:\ for continuous backup and D:\ for every night at 8pm. Other software like ClickFree disregards partitions and backs up everything under one profile.
WD SmartWare took some time to figure out what was going on, but so far everything works great 
