Dear Pete,
Please look again at my first response. There is no way to directly link the output of the Midi Player into the Note On Watcher. But I'll try to be super explicit:
For Mac OS X, do the following:
Go to Communications menu and choose Midi Setup...
In the top left pop-up menu (Port 1, Input, choose Isadora Virtual Out
In the top right pop-up menu (Port 1, Output) choose Isadora Virtual Out
Now if you put a Midi Player and a Note On watcher into the scene, and then start playing the MIDI file, the notes will be sent through the MIDI system of Mac OS X. It will go out of Isadora, and then right back in. In this way, the Note On watcher will see each note coming from the MIDI Player actor.
So, a little roundabout. But it will work.
As far as an "auto-mapping" feature, it sounds like you need to take a look at the MIDI tutorials
http://www.youtube.com/watch?v=E1aj5c-D3U8
and this
http://www.youtube.com/watch?v=2ulA_Ge09hI
Best Wishes,
Mark