Washes can be seem like a miracle tool and to be honest, they are. However, no matter how you apply the wash, be it slathering the entire model with wash or carefully applying it in measured amounts into each individual recess, you are going to need to perform some clean up afterwards.
In many cases, you can get away with just dry brushing the original colour on top, and perhaps slightly repaint areas where the wash has pooled heavily. You can of course try to avoid pooling while washing by carefully 'cleaning' areas where the wash is too heavy. Just allow the bristles of another brush to gently soak up the unwanted wash.
Of course there are some tricks to help with the washing stage. If at all possible you should use gloss varnish on the model before washing it. This makes the model 'slippery', allowing the wash to pool better in the intended recesses. It also tends to extend the drying time of the wash, which in turns allows you to manipulate the wash longer. An unintended, but not unwanted side effect with the varnish layer is that the basic paint job will be more resistant to wear and tear.
Another little trick (advanced painters only!) I've found is to use airbrush paint cleaner to remove unwanted wash. First of all, this requires a properly applied layer of gloss varnish that has been allowed to dry at least 24 hours otherwise the underlying colours will be dissolved as well. Apply the wash as normal, then, just after it has dried, use a brush dipped in airbrush cleaner liquid on any spots where you ´don't the wash. This method gives a great degree of control and is especially useful when painting wash directly into panel lines as you inevitably get some small overflows/spills when doing so. It saves a lot of time since you don't have to repaint all the panels surrounding the lines.