To get the audio-in and out of the VFX software working on the Mac, you need the in and out to be on the same device or sound card. You can do this by plugging in a USB sound card, or by making an 'Aggregate Device' that glues the hardware together. You can not mix your soundcards IO with soundflower 

You can create an 'Aggregate Device' to glue the devices together by following the steps in this link.

If you are trying to use soundflower you need to create an 'Aggregate Device' for both directions, you can not mix your soundcard drivers and soundflower in the same 'Aggregate Device'. Once you have done this the audio should work once you select the 'Aggregate Device'  as the default input and output. Just creating an 'Aggregate Device' is not enough, it also needs to be set as the default device to use in the 'Audio Midi Setup' of the mac control panel.

For routing MIDI from another application into VFX you can use the IAC feature that is built into the MAC OS. Be sure to disable any MIDI drivers that send MIDI from the VFX software back to garage band as the resulting midi feedback will cause the software to crash.

By setting up IAC and soundflower you can use the VFX application like a Rewire application and use plugins that normally only run on a PC.