For an easy setup you do not have to use the sketch from the littlebits-timer as you refer to above.
When you use the Arduino only for one timer setting it becomes much easier.
This is the Littlebits circuit I tested for you, it starts counting directly after powering up:
And this is the Arduino program I used, for different timing you only need to change the counter setting from 90 to another value...
Maybe you can use it...
// Timer with one alarm setting of 90 minutes for Littlebits
// Alex Pikkert October 2016
// Littlebits Arduino Leonardo
// MP3 player I25 connected to digital pin 5
// Power connected to input A0
// After powering up this timer sends only one pulse after
// 90 minutes to start the MP3 player, then waits forever
int AlarmPin = 5;
int counter = 0;
pinMode(AlarmPin, OUTPUT); // sets the digital pin as output
delay (60000); // wait one minute
counter = counter +1;
if (counter == 90) // count 90 minutes
digitalWrite(AlarmPin, HIGH); // sets the alarm on
delay(100); // waits for 0.1 second
digitalWrite(AlarmPin, LOW); // sets the alarm off
goto wait; // waits forever