You are right, khash and network difficulty calculations are estimates. The most accurate way is to measure your rig's baseline share submit rate and try to make a prediction for network difficulty increase.
For example my 2 7950s submitted 3.6 million shares to litecoinpool in 75 hours before the difficulty changed. Share price went from .00000312 to .00000250 and my payout was around 11.5 LTC.
Thanks for the helpful reply
Could you also tell me how much shares I may expect to be submitted on a 1000kh/s rate.