Yeah in my case I only use flangeing / chorus on guitar tracks, and I prefer to use a effect box (Alesis Nanoverb) on the original live guitar track. While it is more flexable to keep the initial recorded signal clean I like to hear the effect as I am playing it, so I can adjust the speed of the "sweep" to match the tune I am playing. Eventually I will just start recording both clean and modified tracks at the same time.