If you go all whole wheat, you need to add about 1 tablespoon of gluten per cup of flour. The whole wheat dough won't be elastic/soft enough without it, which is why they typically add white flour into the mix. If you like dense, hard pizza dough, then you can use just whole-wheat without the extra gluten.
Here's some good information about improving your dough with various enhancers:
Bread Machine Digest » Dough Enhancer’s: And How-To Use Them