Add the zucchini noodles and cook briefly. Place the zucchini noodles in the boiling water and cook until they are tender but not quite falling apart. 1  The exact amount of cooking time will vary depending on how soft you want the zucchini noodles and how dry they are when you start.2  The main thing to remember is simply to keep an eye on them.dd the zucchini noodles to the hot oil and saute sautÃ© them for 6 to 7, minutes stirring. 1  Frequently keep a close eye on the zucchini noodles as they. 2  Cook this cooking method produces noodles that are tender yet slightly crispier than those created through the boiling.  method