Hi Jordan,
Since you're using Final Cut Studio, you can use Compressor to make the multiplexed MPEG2 stream. Unfortunately, the way to create the multilexed stream isn't very intuitive. The option to add the audio to the video is kind of hidden. What you want to do is edit a preset or create your own. Then, under the encoder section in the extras tab, check the Multiplexed button. Here's a screengrab:
For the WMV, yes, use the Flip4Mac Studio Pro. Great software.
I hope this helps!
Jon
TreeLine Productions
Fort Collins, CO USA
Currently producing these popular podcasts: