This is going to sound stupid, but:

If the pc that is running knoppmyth only has 1 serial port, how does the IR blaster work with a remote control?

I mean there has to be "something" that you connect to the pc to read the Remote control IR signal, yes?

I've seen the little serial port connector doohickey that you plug the IR Blater into (that sends the signal to the STB or whatever).

Do you use 2 serial ports then? One for the "receiver" and another for the "blaster"?

Or am I missing something?

Serial port receivers and transmitters use different pins for the received/transmitted signal. It is possible to construct a combined receiver/transmitter which uses a single serial port.

The other alternative is to get a remote with a USB receiver. Or a tuner card where the remote plugs into the capture card.