How do I set up multiple interrupt cycle timers to control separate relays.

you can use my timer library, very simple to use. no delays, small footprint.

after you import the library, check the sample and test it.

/*
      Title: Simple Switch Timer
      Library: sstimer.ino
      Description: 
      Created Date: January 17, 2015
      Created By: Rolly Falco Villacacan
      Released into the public domain.
*/

#include <sstimer.h>

//WATER_PUMP SETUP
int PIN_NO1 = 13;
long unsigned OFF_DURATION = 500; //in milliseconds HOW LONG YOU WANT THE PIN TO BE OFF STATE
long unsigned ON_DURATION = 500; //in milliseconds //HOW LONG YOU WANT THE PIN TO BE ON STATE

//LIGHTHING SETUP
int PIN_NO2 = 12;
long unsigned OFF_DURATION2 = 1000; //in milliseconds
long unsigned ON_DURATION2 = 1000; //in milliseconds


sstimer WATER_PUMP(PIN_NO1, ON_DURATION, OFF_DURATION); //create instance for water pump
sstimer LIGHTHING(PIN_NO2, ON_DURATION2, OFF_DURATION2);//create instance for lighting

void setup(){
//...  
}


void loop(){
//...
WATER_PUMP.check();
LIGHTHING.check();
//..  
}