Trini and Tofu Pup have given you great advice. I use a combination of the crate and a pen. For overnights and when I'm away from the house, puppy goes in the crate. But during the day when I'm here for nap times and feeding, I use a pen which gives her more room. She has a bed in it and some toys and can move around and be more mobile than in the crate. Once the puppy has better control and their schedule is more regular -- around 4 to 5 months in my experience, I give them more time in the pen than the crate, although they continue to spend overnights in the crate.
Keep in mind that puppies don't have control over the elimination muscles until they're 6 months old, so in there are bound to be accidents until then. But as others said, you can control and train by being vigilant and keeping a regular schedule.
