My trick is this... When I first enter a recipe, I use a profile that has my end of boil kettle volume (5.5 for me) entered in the batch volume field with zero losses to the kettle or fermenter. This will make the efficiencies match. From there I switch to a profile for the equipment I will be using. I do the switch with or without using the scale function depending on the equipment and batch size.
I recently switched to beersmith because I feel it has the best chance for future development and is cross platform. That being said, it is missing a lot of features that other solutions offer. Don't get me started on how useless the phone app is.