If you need a frequency output, use analogWriteFrequency() and analogWrite().
If you need periodic interrupts, use IntervalTimer.
If you need both from the same library, get 1.49-beta4 and use TimerOne or TimerThree. In version 1.48, TimerThree doesn't work at all and TimerOne only works partially, so make sure you're using the latest so you have the working versions of those libs.