Wilbur has two erosion tools, a "precipiton" based system that simulates rainfall washing soil downhill, and an "incise flow" tool that calculates water flows for the whole map, and erodes rivers based on flow rates. When using the incise flow tool, be sure to use the "fill basins" tool, every single time. I like to run a few passes of the precipiton tool, fill basins, and then run a few passes of the incise tool, using gradually increasing gradients and decreasing widths. This creates river valleys that are wide near the mouth and narrower near the source.
If your rivers aren't going where you want them to, you can use Wilbur's hill and valley tools to get them to go where you like. On one map, for instance, I created a large, high plateau where all the water drained off the plateau on one side. This created a major river feeding into another major river over a HUGE waterfall. I will often switch back and forth between GIMP and Wilbur in order to use the different tools each provides. The curves and levels tools in GIMP are very useful for fine tuning your contours, using curves for instance you can create continental shelves, flat topped mesas, and sharp spiky peaks.