I believe it is possible to make either IR remote work with any program. I just finished setting up the Hauppauge PVR-150 remote (grey top, black bottom, internal #A415-HPG-A) and I can get it to split the incoming IR signals between mplayer and a shell script I've kind of got working to change channels on the card.
It sounds like you potentially will have 2 IR receivers (one from the Hauppauge card) and one from the case. Ultimately I think you could set up either or both to receive IR signals and do the same thing or different things.
1) Getting a driver into the Linux kernel allowing you to "read" the IR receiver.
2) Setting up one or more lircd.conf (mine are in /etc) files to "map" the numbers coming in from the IR receiver(s) through the Linux drivers into "ascii codes",
e.g. Power, Play, Vol+, Ch-, etc.). Then one must activate the LIRC daemon ("man lircd").
3) Setting up one (or more?) "lircrc" files (/etc/lircrc or ~/.lircrc???) which then indicate how specific ascii command codes are to be handled by each program which interfaces to the IR system.
So for example, I had to play around to get lircd to recognize the command codes from the A415-HPG-A. There are other Hauppauge controller configuration files available on the web but none of them seemed to work for me. There seem to be multiple types of Hauppauge controllers circulating.
Then it took a while to figure out that lircrc controls which programs "receive" which commands. So playing with it one can get Vol+/- sent to mplayer while Ch+/- gets sent to my program that interfaces to ivtv-tune.
If anyone has a Hauppauge PVR-150 which they have working with either tvtime, xawtv (which may be between hard and very hard) or MythTV (which is supposed to work) I would love to get a copy of their configuration files.
I will note that doing this type of hacking for people who have never done it before is time consuming. There doesn't seem to be "Linux IR hacking for Dummies" available.
P.S. contact me directly if you want my configuration files.