I did a time entry like you mentioned.
input 9am to 6pm which gave me 9 hours total. After that i added 1, 2, 3 hour breaks, noticed the stop time got incremented by the same amount of break time added 1, 2, 3 hours. So start time 9am and stop time 7, 8, 9pm, which kept the total hours at 9 hours.
thanks,
Rad