which IDE for DUE?

Hi,
I'd like to do some fast (40kHz) PWM on some channels on a Arduino Due.
What is the right IDE/toolchain for that? After googling a day it looks like this:
Normal Arduino IDE works fine, but fPWM is 500Hz. If I want an other I have to
use AtmelStudio6 with ASF. (But there I was unable the get the communication
via avrdude running).
Is there no simple and easy way to do it in the standard IDE?

joh