Here's what the Syntrillium people wrote back to me
Hi, Cool Edit can be midi-triggered by sending either Midi notes or Controller numbers. To be able to control CE with your Yahama, you would have to know what controller number your multitrack is sending out that corresponds to each of it's functions. In other words, if the 'play' on your MD corresponds to midi controller 4, you would simply go into Cool Edit and go to Options>Shortcuts, select 'Play/Stop toggle' (for instance), click the Enable Trigger check box, set the midi channel, and then select the Controller box and set it to controller number 4. Controller numbers can also have 'values', though if the function is not a variable one, the value is usually defaulted at 127 (or 128 is some midi systems).
Basically, you need to find out if your Yamaha has controller numbers assigned to it's transport functions and then you can 'trigger' Cool Edit. If you are looking to Sync the two together however, Cool Edit can only act as a Slave device, and your Yamaha would have to be able to generate the necessary time code for syncing.
---Syntrillium Support