Beersmith will not automatically CHANGE your equipment profile or your recipe efficiency. It will calculate your actual efficiency, if you put in your actual numbers for "measured" parameters. But, its up to you to decide to update the recipe/equipment parameters (if you want).
It does require trial and error to get the number right for your equipment and methods. Its usually best to start low (maybe 60-65%) and adjust upwards as you learn what your actual yields are. I generally adjust by 1/2 of the difference when learning a new setup. Eg. I might start at 70%, then make a couple beers and get 80%...so, I might adjust up to 75%, and make a couple more beers.
I find it easier to adjust for a better than expected extraction, than for worse than expected. Its easier to add water than go get some DME and mix that in.
When you create a new recipe and select your equipment profile, beersmith will default the recipe efficiency value to the value in the equipment profile. But, you can change it after that. As long as you don't change equipment profiles, the efficiency value will not change.
Finally, you will probably find that your actual efficiency is a function of the target OG. Bigger beers will be less efficient than smaller beers. I use different efficiency values for every 10 gravity points of OG. Eg:
1.030-1.040 = 80%
1.040-1.050 = 75%
1.050-1.060 = 70%
1.060-1.070 = 65%
...etc....
Those numbers are pretty close to the actual numbers I get on my system for those ranges.
Generally, I have my bank of recipes...and I have my brewlog folder. I copy a recipe to the brewlog on brewday to record my actuals for that batch. Then, I will take those actuals and calculated results and decide how to go back and update the original recipe....including any efficiency changes, and the resultant necessary ingredient changes to compensate for the actuals. I may or may not change the version number and save as a new recipe...depending on the magnitude of the change. If its just tweaks the grain-bill to compensate for efficiency, I don't usually update the version.