I crate trained both of mine as well, and they continue to sleep in the crates at night and when we leave the house. They really love them, and run in there when I say "go to bed".
When they were little pups, I would put them in the crate various times of the day/night with some chew toys, etc. to get them used to it. Always make it a happy experience with a little cheerio or piece of kibble. NEVER use the crate for a place of punishment. I would leave the room too, so they wouldn't see me and whine. When they were left out to play, I only gave them access to the kitchen and family room- blocked off with baby gates. It is much easier to keep an eye on them in a small area. Usually they will circle or sniff around before they have to pee, and when you see this, say "outside" and scoop her up quickly and head for the door. I still take them out to go on a leash, that way I know for sure they are going. She will need to go out every 2 hours or so since she is so young. Be patient, puppy training is the least fun, but her never ending love and devotion is the BEST.
Jato - Blenheim, Nov. 2007
Zoey - Ruby, June 2008