IR-commands cannot be sent to the serial port.
I hacked the IR-driver so that any process running on the empeg can write an IR-code to /dev/ir, which gets passed to any application reading /dev/ir; in this case the player application.
I also found out it was possible to fake incoming serial data from applications running on the empeg.
Some serial commands:

n: next song
q: quit player and start shell
#fid: start playing MP3 with specific fid

There's a more complete list on the developer site.

Frank van Gestel