I'm not a beersmith user, but my understanding is that the mash profiles affect the fermentability of the wort, but have very little (if any) impact on the original gravity.
Anything that happens after the boil will not affect the IBU's, but it is possible that the gravity of the wort during the boil could affect them (although this is subject to some debate).
The most commonly used methods for guesstimating IBU's are Garetz, Rager, and Tinseth. There are others that I have not yet researched.
Norm Pyle's Hops FAQ gives some information on the various methods, but I have no idea how accurate this information is.
FWIW, I use Tinseth, because Promash supports it, and it usually falls between the other two.
Whatever method you use, they only provide estimates, and the real values will vary according to the equipment and procedures that you use.