The controls for the mux are GPIO [0,1] for source, and GPIO 2 for muting.
  
  GPIO0  GPIO1
    0        0    TV Audio
    1        0    FM radio
    0        1    Line-In
    1        1    Mono tuner bypass or CD passthru (tuner specific)
  
  GPIO 16(i believe) is tied to the IR port (if present).
  
  ------------------------------------------------------------------------------------
  
  >From the data sheet:
   Register 24'h20004  PCI Interrupt Status
    bit [18]  IR_SMP_INT Set when 32 input samples have been collected over
    gpio[16] pin into GP_SAMPLE register.
  
  What's missing from the data sheet:
  
  Setup 4KHz sampling rate (roughly 2x oversampled; good enough for our RC5
  compat remote)
  set register 0x35C050 to  0xa80a80
  
  enable sampling
  set register 0x35C054 to 0x5
  
  Of course, enable the IRQ bit 18 in the interrupt mask register .(and
  provide for a handler)
  
  GP_SAMPLE register is at 0x35C058
  
  Bits are then right shifted into the GP_SAMPLE register at the specified

  rate; you get an interrupt when a full DWORD is received.

  You need to recover the actual RC5 bits out of the (oversampled) IR sensor
  bits. (Hint: look for the 0/1and 1/0 crossings of the RC5 bi-phase data)  An
  actual raw RC5 code will span 2-3 DWORDS, depending on the actual alignment.
  
  I'm pretty sure when no IR signal is present the receiver is always in a
  marking state(1); but stray light, etc can cause intermittent noise values
  as well.  Remember, this is a free running sample of the IR receiver state
  over time, so don't assume any sample starts at any particular place.
  
  http://www.atmel.com/dyn/resources/prod_documents/doc2817.pdf
  This data sheet (google search) seems to have a lovely description of the
  RC5 basics

  http://www.nenya.be/beor/electronics/rc5.htm and more data

  
  http://www.ee.washington.edu/circuit_archive/text/ir_decode.txt
  and even a reference to how to decode a bi-phase data stream.
  
  http://www.xs4all.nl/~sbp/knowledge/ir/rc5.htm
  still more info