So first of all you need to understand that BS is a tool to HELP you make your brew day easier as well as handling all your calculations for your recipe....
BTW, I'm not trying to be an a$$ hat, just trying to help
Everything bS does is based off your equipment profile so step one is to get the right profile set up so go to the equipment profile tab and select a pre set option that most closely matches your set up.
Look through that set up and change items that you KNOW to be different like boil off and losses. BS also uses I believe .21. For absorption. You can also change default values like how much you want to mash in with whether it be 1.25, 1.5 qts/lb ( I don't remember where to go to change these)
Once your profile is close, then put your recipe in. Note. Some values may differ a little based upon the software's default values for potential extract and SRM and hop AAs,etc. you can change these as well in the various tabs.
Brew: when you brew take notes pertaining to losses and other variables associated with your profile, then go back in and tweak those values.
It will take you a few batches to get things dialed in and then everything will be easier.
In addition, their website has great tutorials on all this stuff
there are also numerous threads in the software forum!