Hmmmm, this is a really good question, and I look forward to reading what others do. Having said that, I'll offer my own preference;
1-if I am really committed to what I am hearing from the VI plugin, I will likely commit it, just as it is(probably with following plugins kept "live")
2-re VI plugins in general, I(personal choice) often don't use the built-in effects, and will choose my own in the same way I treat real instrument processing. Why? Mostly because, by choosing my own effects, I can create an overall sound that is not a carbon copy of the thousand other users of that same VI(example: Superior Drummer has a bunch of ambient and room sounds, which I usually leave off. I use my own "drum room" (from my choice of plugins that include Avid SPACE, IK Classik Room, Eventide T-verb, Abbey Road Chambers) so my drum tracks, done with SD don't sound exactly like the next hundred SD users
