There's only one set of FX units.
When in patch mode, the sounds can use all 3 of them. However, in Perf mode, you have to tell the JV what fx setup you want to use. The one you choose will be accessible by all the channels, but, of course, they will sound different to when played in patch mode.
If you put Synth/Pad 032 on midi chan one, and tell the JV (using sound diver for example) to use channel one's fx setup for the performance, and if channel one's output is set to the effects output, then it should sound the same as in patch mode.
Sorry, I didn't put that too well.. hope it helps.