If you entered your gravity and volume readings into BeerSmith, it will have calculated your Mash and BH Efficiency on the 'session' tab. You can start with adjusting your equipment profile to reflect the calculated BH efficiency. Next, with your pre-boil and post boil volumes and the boil time your used, you can calculate the boil off rate and correct that in your equipment profile. Other changes to the trub loss should be adjusted to reflect your actual results in the new equipment profile.
Assuming you have accounted for all your other losses correctly, you can make a copy of the recipe you just brewed and upload the corrected equipment profile into it. If you are close, it should adjust the expected outcome to be close to your actual results. The volumes BS2 is recommending for your mash and sparge (if you conducted one) should also reflect any changes you made to bring you closer to your desired results.