I've yet to find a package that can effectively log and display what you intended to brew vs. what you actually brewed (e.g. planned 1oz 4% Cascade and during brew found only 1oz, subbed .5oz 8% Centennial). As a LOT of us do brew-day-substitutions, that would be a handy feature to find (is that in BS2?).
It was in Beersmith 1 as well...
On brew day, select your recipe and click the button that says "copy to log".
Go to Brew Log, and double click the recipe you just copied to open it. Click on the date field and set the date to "today".
Now make whatever changes you want to ingredients, mash, etc. for this brew using whatever substitutions or process changes you have for that session. Use the notes field as appropriate for logging brew day notes that don't fit into one of the predefined fields in the ingredients, mash, water, etc.
The Brew Log should be your log of what you have actually brewed, as opposed to the Recipes section which is what you should use to design recipes.
I don't think the documentation is very clear about the difference between the two, or the process you should use with the software, but that is what I have done for several years and it works well for me. For each brew day, I have a separate copy of that recipe in the Brew Log with specific changes/notes based on what I did that day.
There isn't really a good "comparison" where you can view deltas between the source recipe and the brew log, though. However it wouldn't be too tough to make something quick & dirty using a diff tool.
I keep hearing people complaining specifically about that "missing essential feature" but it is because they don't know how to use the software, not because it isn't there. I think Brad could do a much better job at making certain aspects of Beersmith much more intuitive, and that is definitely one area that could use some improvement...along with simplifying the UI in general.
