My setup is a little more complicated than you've detailed, Tony, but the principle is exactly the same (I run one bass with audio and midi signals).
There are a number of complex problems, but if you've got midi experience you should be able to sort it. It obviously goes without saying that the more complicated you get, the more problems arise.
My setup is:
Midi:
Bass (GK3b) => axon ax100 => fcb1010 => Novation Supernova => Korg Microkorg > (audio) LS2.
Audio:
Bass => Bass POD => EHX Bass MicroSynth => ZVex Woolly Mammoth => MoogerFooger Lowpass => DL4 => LS2
But with some complicated wiring. My tone sucks ass, but my sounds can destroy buildings.
Dan