You can create AppleScript's that do things such as play/pause, next track, previous track and then using the microsoft keyboard pref panel set the key settings for the media keys to use command "Open Item" and then choose the apple script that corresponds with the media key you wish to use.
Here is a link to what the apple scripts should look like. http://www.jack.sh/2011/07/21/spotify-applescripts-0-5-2/
Honestly, I simply opened Automator, create new application, added action "run appleScript" and for the area where the script goes, added:
tell application "Spotify" to playpause
Next, I assigned that application to the play/pause media key.
For next track and previous track the script should just be
tell application "Spotify" to next track or tell application "Spotify" to previous track
Hopefully this helps anyone struggling with this.