Reading a pin as an input on AVR XMEGAs
There are a few concerns I have.

1) Unless you start counting pins from 0, (1 &lt;&lt; 5) is actually pin 6.

2) According to the code, pin 6 going high causes the LED to turn off.

3) Immediately after turning the LED off, you turn it back on.  Turning it back on should probably be in an else block.

4) This part of your question is confusing.

I wanted to do the same thing just instead of when pin6 goes high I would like to have pin 6 go low and turn on the led on pin5.

The reason it is confusing is because you say that pin 6 is an input, and then you say you want to drive pin 6 low (which implies an output).