Rarely is a three way timer switch (if such an animal exists) useful. But a regular timer switch can override a 3 way switch setup to do one of: hold the light on all the time or keep the light off all the time.
When the timer is overriding the 3 way switches, you cannot easily set the 3 way switches so the light does what you want when the timer stops overriding, except if you remember which 3 way swithc positions do what.
Stick to your lawn watering schedule until it really starts to pour. After the storm you have only the same number of rest days you always had and then you need to start watering again.