First off, my workflow: I write with MIDI, tweaking parts and arranging. I keep my MIDI and softsynth Audio tracks separate too (mostly because I oft times use multiple MIDI tracks for the same synth).
When I reach the point where the song is ready to mix, I render all the MIDI into separate audio tracks. After a little housekeeping (archiving the MIDI and softsynth audio tracks, re-org'ing my folders and whatnot) I then have clean audio to work with where I build my mix up.
So, the rendering process: I do it track by track. Selecting the MIDI track, soloing it, selecting the corresponding soft-synth audio track (It's one of my biggest gripes SONAR can't auto-detect this btw) and bouncing it down to a new track. Then I re-name that track, re-route that track (to it's corresponding bus) and move that track to it's corresponding folder. It's a bit tedious. I've long suspected I could bounce down multiple tracks to separate audio tracks but experimentation seems to indicate that't not possible? Is there any other shortcut for rendering all the MIDI tracks to discreet audio tracks?