After I've programmed EzDrummer and recorded all my guitars through either Line 6 POD Farm og Amplitube, as well as recorded other synth sounds, I usuallly bounce them when I move from recording to mixing, siply to "commit" to those sounds, just as if they had all been recorded live (Real drums, real guitar amps, real piano/strings/organs/etc.).
Just how I prefer to do it :)