I have also marked my plastic stir spoon with volume graduations based on my boil kettle. I used a file to mark the graduations and highlighted them with a sharpie with no ill effects.
Back on BeerSmith - BS uses to entries to calculate mash efficiency. 1) Pre-boil Gravity and 2) Pre-boil Volume. So, by increasing (or decreasing) either one of these numbers will dramatically change the mash efficiency presented in BS. So, in my opinion, you first need to dial in your Equipment Profile within BS. That said, a good grain crush, as the other brewers have pointed out, is vitally important. However, in BS, if the software thinks you have a 75% efficient BrewHouse, then it will project all your SG’s based on that factor. So, if your BrewHouse efficiency is, in reality, actually more like 65%, than all the numbers start to collapse, starting with the Mash efficiency since that’s the first real measure of efficiency the software presents.
So, assuming the grain crush is perfect, if your Equipment Profile within BS is not accurate, neither will the projections and estimates.