Watch this video about house training using a crate. It's only 5 or 6 minutes and it all becomes clear :)
Take a look at this video on YouTube:
He's got lots of positive training and clicker training videos and they're always very easy to follow.
If you get interested in clicker training, 'click for quiet' can be useful for a dog or puppy who will cry for hours before giving up....as others have said the golden rule is never open the crate when they are crying or whining.
You have to 'load the clicker' first (teach the puppy what a click means) and there are lots of articles and videos if you google.
Click will mean - correct! Treat is coming!
Once you've taught that you can work on the crate. Get him happy in there by shaping. 'Shape' him going in there by clicking and treating when he goes near the crate or looks at it and eventually going in there. Click when you can shut the door half way for a second and build up the time.
With the door closed, click and treat when he's quiet, initially you will have to be quick, every few seconds. Wait for him to take a breath from crying and click and treat. Start building up the time he has to be quiet for - 1second, 2seconds, 3seconds. The smaller you make the steps, the quicker it is!