Compensate by adding less hops. IBUs in beersmith should just be used as a reference for your personal tastes. If you think the beer is too bitter then lower the IBUs by either reducing the amount of bittering hops or reduce the flavor/whirlpool hops you are adding. The only way you are going to fine tune your system is by using a consistent process and brewing a lot. Figure out what you like and match it to your IBU calculations.
Also, if you can always wait 10 or 20 minutes for the temp to drop before adding the whirlpool hops if you think its adding too much bitterness. In any case, consistency in your process is key.