I'm not quite sure I completely understand what you're asking. But from what I see, if you're trying to make a break in the circuit, I guess you could just add a switch between the battery terminal and the arduino you use.
I don't know if you can add a delay in the setup though? Otherwise you might be able to do something like:
const int motorPin = 3;
void setup()
{
pinMode(motorPin, OUTPUT);
digitalWrite(motorPin, LOW);
delay(180000);
}
void loop()
{
digitalWrite(motorPin, HIGH);
}
If it helps I recommend going through some of these:
http://oomlout.com/a/products/ardx/
There very easy to do, and fairly easy to understand how things work and what you do to use what. For example the delay functions and motors.