OK, let's walk through the process and key measurements.
First is an accurate measurement of your water inputs: total water (initial infusion + sparge water) into the mashing process.
Next is a good measurement of your wort volume collected from the mash process. The difference of water input and wort collected is your water retained by the grains and any dead space in your mash tun. Subtract your mash tun dead space and divide the result by the weight of grains used and you have your grain absorption factor.
Step 2, the boil off rate: If you top off any water into the kettle before the boil, you need to have a good measurement of this. The pre-boil volume minus the post boil volume is your volume loss in the boil. This value divided by the time of your boil is your boil off rate.
Now look back at your past brews. If you filled out the volumes and gravity readings you took in the 'session' tab, BeerSmith will calculate your actual mash efficiency and total efficiency and report the actual on the 'session' tab. It is often best to use an average of those brew sessions that you have the most confidence in your readings.
Use these figures from BeerSmith (Brew house or total efficiency from the 'Meas Efficiency' on the sessions tab), along with your calculated values (your boil off rate, and your grain absorption rate) to create a new equipment profile. The grain absorption is actually a global setting which can be found under 'options' > 'advanced' > 'grain absorption'
This should help you get the BeerSmith prediction closer to your measured values. Use your next couple of brews to update these values and the software should quickly come into agreement with your process readings.
The more accurate your measurements and consistent you conduct your brewing, the faster this process will occur.
