The VST effects are applied to the audio outputs, not the source MIDI parts. So for USB you have 2 pairs of outputs at your disposal.
For example, if I want a specific effect on one pafrt, then Ill asign that part to USB2 out, and leave everything else on USB1.
Of course if you need more than 2 different types of processing, then of course you will have to bounce to audio (or use analog outs as well) - no way around that on any synth once you run out of separate outputs (typically I have different processing for every part, so I bounce to audio quite alot, but if you used to using hardware synths - thats normal).
If you are using analog outs, then at you have 3 output pairs for patching to your mixer or other hardware. If you take the trouble to do manual per-part sync compensation (if your software allows this - cubase sx for examples does) then you can get uotp 5 output pairs, or get a bit more creative and use some mono outs as well to give you 10 mono outputs in total.
To keep analog outs in sync with USB outs, you have to delay the analog outs by as much as 40-60 ms depending upon your sound card and TI sample rate.
Personally - I rarely bother with more than a couple of output pairs and use out 3 + inputs as a TI version of the model C aux bus, choosing to bounce to audio instead.
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