Download the manual and look at page 171. You want the FRQ waveform generation at the bottom of the page. Elsewhere in the chapter, you can see how to enable the pin you want to toggle.
The device runs at 2MHz by default, which is just fast enough to toggle the pin. You can change the clock to 32 MHz.
EDIT after question modified.
I see you are using the Atmel Software Framework. I don't have much experience with it. It still looks like you are not using ASF correctly.
You said you want to toggle a pin every 1 us. Is that correct? Perhaps you should be more specific in your question about what you are trying to do.
The difficulty with that fast frequency is that the clock on the device runs only a little faster than that frequency. This indicates you should not use an ISR (interrupt service routine). The routine will take too much time to run, and will not be able to achieve the 1 MHz frequency. (In any case, an ISR is meant to respond to an interrupt, not to be called from main()
.)
But you can achieve the pin toggle without using an ISR. Instead, let the clock toggle the pin directly. Use the FRQ functionality. You set the period in a register, and connect the clock to the correct pin using the event channel system. The details should be in the manual.
Do you have to use the ASF? Configuring the clock and processor speed is easy to do without it. Just assign certain registers to the correct values in your own C code.