what kinda pup do you have?
if it is a mix..
how big is she/he?

You absolutly DONOT want to get your pup into the habbit of peeing or pooping in the crate.. that is his/her "DEN", he/she will sleep there and spend tiem there when you are away (at school or work).

To avoid having your pup go to the bathroom in the crate, make sure you have schedualed bathroom breaks for your puppy.
About 15-20 min after your puppy eats or drinks take it outside. and wait till he/she goes to the bathroom.. Then reward...

Until your dog is housetrained, s/he should not be allowed free run of your house. Otherwise, s/he will develope the habit of leaving piles and puddles anywhere and everywhere. not pleasant.. I know

If you ever find an accident in the house, just clean it up. Do not punish your puppy... Its your responsibility to keep an eye on your pup...

Hope I helped...