Well I figured out that irmanager -d 1 means discovery on (I guess same as echo 1 > /proc/...../discovery). But that's all I really found out about it.

Well thanks for your help, I'm done trying to get this to work tonight. This does have some interesting applications for me though. One thing... Does IrDA traffic conflict with consumer IR? That is, if I had an IrDA link between the Empeg and the PDA, would I still be able to use my remote? If not it'd be a little less useful...