OK, here's a quick run-down on what you need to know...
In a typical IR scenario, there's optical transmission (from IR LED to to IR receiver), and then the wired transmission (through a distribution network, or into devices that have a 3.5mm IR control input jack for instance).
Optical transmission uses a 38kHz (depending on the standard, but this is common) square wave that is pulsed on and off to send the data. In other words, when the LED is "on", it's actually flashing at 38kHz. When it's off, it's completely off. This is called the 38kHz "carrier", and is used by the receiver to tune its reception to a specific frequency, rather than accepting the random presence and absence of infrared light as a potential signal. This avoids false triggering from sunlight or other sources of IR.
To replicate this, you would use a 38kHz PWM output that is turned on and off according to the bits you need to send. That's what IR LED transmit libraries do. Clear on that so far?
When the signal is received, it can be done either through a photo-receptive component that is capable of sensing infrared, or an IR decoder. With the former, you get an analog signal that is an electrical equivalent of whatever IR energy exists. But the latter is a photo-receptive component plus just enough smarts to detect the 38kHz carrier and only respond when the carrier is present. Flash an IR LED at it with random time periods, you get nothing on the output. PWM at 38kHz and pulse that on and off, you get output which mirrors the on/off pulses (without the 38kHz carrier superimposed).
The IR decoder should have three legs -- Gnd, Vcc, and Out. When it detects a 38kHz signal, it will pull its output to ground on the low periods of the signal, and let the output float on high periods. So, the device reading the decoder's output (e.g., your distro amp) has to set the "high" voltage through a pull-up resistor for there to be both high and low states. Make sense?
If you try to drive the amp (wired protocol) via a sketch intended to drive an LED (optical protocol), then you end up throwing a 38kHz signal at the amp, which it will not know what to do with. Depending on the intelligence of the amp, it may just broadcast it (modulated again by a 38kHz carrier on the outputs, leading to pulses of light corresponding to the intersection of the two 38kHz oscillators), or reject it (if the signal is received, buffered, and re-transmitted), or who-knows-what. Also, since the Arduino output will likely drive the line both low andhigh, you'll impose the Arduino's Vcc (likely 5v) upon the amp input as the idle condition. This is likely to cause problems. Probably not fatal problems, since it will probably be current-limited enough to shunt away overvoltage (if the amp idles higher than 5v) at the pin's input protection diode, but it will likely interfere with normal signal distribution regardless.