I used to do double chances with the add-on or rebuy button, but now I just set the total chips to the total and each players stack includes a double chance chip, so in your case it would be 9,000 initial chips, including the early bonus, and I would just register everyone with 9k and then make a chips in play correction once started for those that didn't get an early bonus.
Nothing wrong with the way your doing it though! I think you will probably find it is a bit counter productive though
Regards
Stuart