When opening a novaLogic mission extracted from the PFF The only way I could get the commands was to open the map then open a second map and copy and paste the existing wave commands from P1 to P2
I've uploaded a mission called Operation Blackwatch (below) that has some commands for the wave files to play.
Here's a link to a bms to mis converter, to get the bms files, most pff extractors will work.
http://novahq.net/files.php?ID=331