Hi Kon,
PitchFactor will work both in front of the amp and in the effects loop. These two choices have different sounds. In front of the amp is a dirtier sound and might be a good choice for heavy sounds like factory Presets 30:1 through 31:2.
In the loop is the cleanest way to go. You could try experimenting changing the order of PitchFactor, TimeFactor, and ModFactor in the loop for sound variations.
Personally I would start with PitchFactor first in the loop, then TimeFactor, then ModFactor and see how you like that.
That's a killer rig you'll have there!!
Alan