How can I prevent the whole-house fan from blowing the attic insulation into the soffit area?

If the whole-house fan is blowing the insulation into the soffit area it may be too close to the roof deck.

If a whole-house fan is moving insulation around inside the attic it generally is a result of the fan being too close to the roof deck. The flow of air is being pushed back down from the roof deck and the velocity of the air is enough to pick up the insulation and move it out to the whole-house fan's exhaust points which includes the soffit area (attic intake vents). Adding a box around the whole-house fan which directs the air straight up, as opposed to outwardly across the insulation, will help minimize the air velocity above the insulation.