1. Cut zucchini and yellow squash lengthwise into 1/8-inch-thick slices, using a mandoline or sharp knife. Spread zucchini, yellow squash, and onion in a single layer on 2 parchment paper-lined baking sheets. Sprinkle with salt. Let stand 1 hour. Transfer to a colander, rinse, and drain. Place in a widemouthed 1-qt. jar, filling to 1/2 inch from top.
2. Bring vinegars to a boil in a medium saucepan over medium heat. Add sugar; cook, stirring constantly, 3 to 5 minutes or until dissolved. Stir in next 3 ingredients. Bring to a boil, immediately remove from heat, and pour over vegetables. Cool 1 hour. Cover and chill 3 days before serving. Refrigerate up to 2 months.