Okay the thing is:
Frusciante uses the wah after distortion (which is kinda rare thing to do) cause the DS-2 has an extremely defined and strong midrange. If you put the wah before DS-2 the wah effect is very mild and hard to notice cause the DS-2 will fill all the tonal gaps.
Put the wah after DS-2 and you will get the frusciante tone immediately and a very stong wah effect. In this case you need to max the DS-2 level (like Frusciante does) which adds bass and softens the otherwise a bit harsh tone.
Ps. You wont get the Frusciante-sound with tweed amp etc. You need to have marshall'ish amp to handle that DS2-WH10 -midrange mayhem.