The trick to prep is mise en place. Get all of your ingredients, pre-measure, have everything that you need before you need it.

The dance of trays in and out of the oven is something rather unavoidable unless you've got enough trays to batch out all of your dough at once, and adequate counter space to rotate trays and let things cool properly. How many baking trays do you have? Cooling racks? How much counter space?