Moving away from the software question (though I will add that I, too, like Beersmith) it sounds like you fermented for two weeks and then racked to a secondary where fermentation continued prior to packaging.
If that's the case, you simply racked before fermentation was complete. Rather than try to stick to a set fermentation schedule you should let the beer ferment until it is complete. In this case, maybe start taking gravity readings at two weeks and package when it is stable. It's stable when it's stable, whether or not that matches the initial prediction.
There is no real need to rack to a secondary and many of us regularly do not. There are reasons to do so (dry hopping, add fruit, bulk aging, etc) but in most cases it is unnecessary. My beers typically sit in primary for about four weeks and then go straight to the keg.