Here is the method I use to set my RTC, it’s primitive for sure but simple and effective. I update the fixed values in the setup function for a time ahead maybe 3 mins. Then I upload the sketch to the board. Note that it waits for any character to be sent from the serial monitor before actually preceeding to set the RTC. Then I call up one of the many time reference web sites that have a running time clock being displayed. So when the web site time matches the time I preset into the sketch I hit a character on the serial monitor and the time gets updated in the RTC and the main loop just keeps printing the time data after that. So nothing fancy but I like being “part of the loop”. 
Lefty
Note that this was written using IDE ver22 and might need tweaking for IDE 1.x ?
/*Reads the value from a Real Time Clock (RTC) DS1307 and displays it in the serial monitor
*
*Created by D. Sjunnesson 1scale1.com d.sjunnesson (at) 1scale1.com
*
*Created with combined information from
*http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1180908809
*http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1191209057
*
*
*Big credit to mattt (please contact me for a more correct name...) from the Arduino forum
*which has written the main part of the library which I have modified
*
*/
#include <WProgram.h>
#include <Wire.h>
#include <DS1307.h> // written by mattt on the Arduino forum and modified by D. Sjunnesson
void setup()
{
Serial.begin(57600);
Serial.println ("Hit a key to start"); // signal initalization done
while(Serial.available() == 0){}
// Hit upload about 10 seconds before selected time
RTC.stop();
RTC.set(DS1307_SEC,0); //set the seconds
RTC.set(DS1307_MIN,28); //set the minutes
RTC.set(DS1307_HR,23); //set the hours note 24 hour clock
RTC.set(DS1307_DOW,5); //set the day of the week
RTC.set(DS1307_DATE,13); //set the date
RTC.set(DS1307_MTH,1); //set the month
RTC.set(DS1307_YR,11); //set the year
RTC.start();
}
void loop()
{
Serial.print(RTC.get(DS1307_HR,true)); //read the hour and also update all the values by pushing in true
Serial.print(":");
Serial.print(RTC.get(DS1307_MIN,false));//read minutes without update (false)
Serial.print(":");
Serial.print(RTC.get(DS1307_SEC,false));//read seconds
Serial.print(" "); // some space for a more happy life
Serial.print(RTC.get(DS1307_DATE,false));//read date
Serial.print("/");
Serial.print(RTC.get(DS1307_MTH,false));//read month
Serial.print("/");
Serial.print(RTC.get(DS1307_YR,false)); //read year
Serial.println();
delay(1000);
}
