I do both. I formulate recipes and test concepts in Beersmith. I keep all of my master recipes (including the ones I've downloaded or adapted from other sources) in the main folder. I keep the "as brewed" recipe in the Brewlog folder. That lets me check how I've changed each batch from the master due to LHBS availability, experimentation or the brew day not working out entirely as planned.
For brew day I print out the brewsheet from Beersmith. It provides a handy checklist so I don't forget things like adding a Whirlfloc tablet or first-wort-hopping. I scribble notes on the brewsheet as things progress -- times, quantities and gravities of each of the mash runnings, overs/unders on amounts or temperatures, amount of Kettle Krud (tm) left, etc. On the back of the brewsheet I keep notes on the progress of the fermentation -- time to airlock activity, ambient and fermentation temperatures, taste of hydrometer samples, that sort of thing. This gives me a physical record that is much easier to reference for future brew days.
For example, my next experiment is parti-gyle brewing. I'm going to make a big beer from the first runnings and a smaller beer from the 2nd/3rd runnings. Reviewing my notes for the last couple of batches I can tell that for a given recipe I'll get 10qts of 1.075 - 1.080 wort from the first runnings. That's pretty handy, and not something you can easily track with the existing software.
Chad