You should be able to set it up so that the input from your mixer gets sent into PD. Just click the media tab, go to audio settings, and make sure that your input device is the mixer. In your patch, you can create an [adc~] object; the outlets in this object will send out the signal from your mixer.
In terms of manipulating the sound, there are a lot of things you can do. One thing I like to do with guitar is to set up a bunch of delay lines (using [delwrite~] and [delread~]) with different lengths and levels of feedback, and then mix them all back into a final output. (Here is an example of what it sounded like the last time I tried it: )
I'm also trying to experiment with using Ben Saylor's [partconv~] object; it convolves one signal with another, meaning that the frequencies of each are multiplied and you will hear only the frequencies that are present in both signals. It's a little bit hard to explain, but if you want to play with it I recommend opening up the browser and finding the [partconv~] help under bsaylor/ in the 5.reference/ section.
Anyway, good luck experimenting!