Hmmm ... I don't have my laptop with me at the moment, so I can't see what irmanager is doing, but I believe you can just ignore the "irmanager not running" message. The switch to irmanager is simply "start" (assuming it is a shell script living in /etc/init.d (Debian style), or somewhere else if not Debian).

irda0 coming up is a good sign. Actually, if you now try to flash your PDA in front of the Empeg (with IR transmission happening), you should see the RX or TX (or both) packet count increasing on the irda0 device (do an "ifconfig irda0" and verify if the packet count increases over time).

Regards
Amit