After Mini V3 is inserted as an audio FX, the track's audio is automatically directed to the plugin by SONAR. You just need to switch Mini V3's external input on. Here's a quick test I just did to verify:
1) Solo an existing audio track. Press play to confirm that you can hear the track. Keep the track playing.
2) Insert Mini V3 into the FX bin of the track. The track should go silent. Keep the track playing anyhow.
3) In the Mini's Mixer section, turn External Input Volume knob to Max and use the switch next to it to turn the external input on.
4) Turn off the other four switches (to get rid of the synth's default preset).
5) Press and hold a key on the Mini's virtual keyboard. Can you hear your audio track?
Again, I'm using the VST3 versions of the plugins. If you have installed the VST2 versions, they may behave differently.