It's pretty easy. Format a DS/DD floppy at 720K on you PC by running this in DOS (Start -> Run):
format a: /n:9 /t:80
Put the floppy in your Atari and save the .mid files onto it.
The floppy will be readable in you PC.
Alternately, you can use the Gemulator Explorer to browse your ST floppies on your PC. I found that you have to copy over one file at a time though, but it works: