Preheat the oven to 400 degrees F.
Toss the squash with 2 tablespoons of the oil and season with salt and pepper. Roast, stirring once halfway through, until the squash is just tender and golden, about 30 minutes. Remove from the oven, and cover to keep warm.
In a small bowl, whisk together the vinegar, shallots, lemon zest and ginger. While whisking, slowly add the remaining 4 tablespoons of oil in a slow, steady stream until the dressing is thickened and emulsified. Season with salt and pepper.
To serve, in a large mixing bowl, toss the watercress, warm squash and pomegranate seeds with the vinaigrette until coated; transfer to a serving platter.
Serve while the squash is still warm.