Can I use more than one Flirc in one Machine?

Yes. 2 Flircs will appear to the computer as 2 USB keyboards.

When programming the Flirc devices, only have one connected at a time.

You can then program each Flirc to respond to a different remote controls, e.g. you could have one remote for Plex and another one for Boxee whilst leaving both Flircs plugged in at all times.