That's what I do when I'm using Cubase SL - create a separate track with the midi metronome sound. Then you can mute it at a later stage. I think this very subject came up on the CC board a little while back.
I know Cal uses Cubase too. He may have a different way of doing it.
It's certainly possible to create a new audio track and record the external synth sound in through your sound card whilst muting all other tracks.
Andy