I would not suggest letting your puppy pee or poop in the crate. It will only confuse her and TEACH her that that is the place to go potty. Immediately start with the pee pads. Be sure to praise and reward her when she goes on the pads so she knows she is doing the right thing. Hope all goes well!
Oh yeah, crate training isn't ba, just not training that the crate is the potty! Putting your baby in the crate at night and for intervels during the day is a wonderful idea and really helps in other areas.