Okay, I'll do my best to help... hope this all makes sense and everything... just tell me if I ramble or don't make sense, okay, sometimes I do that...
Anyway, both of our dogs are kennel trained. Shyla is a 4 year old american husky and Pepper is a 5 year old sheltie cross... he is a rescue pet and was already trained but we got shyla at a few months and we moved into the city when she was about 1 or 2 and we had to train her then....
She was actually pretty easy... and Pepper, when he came to us had to get used to it again but we found out he was trained already.
Now, the first thing you should remeber when training a dog to a kennel is that they should feel at home in the kennel... and not be afraid of it... so make it comfortable, maybe put some blankets in it and when your dog is in their kennel comfort them... it doesn't have to always be for travel that they are in the kennel for... it can sometimes even be a place to sleep or feel safe in when you are in a strangers home.
to answer your questions
1. What is the point of crate training- is it for denning and safe place? is it to keep him in with the door closed? time out area? i found myself unsure
The point is different for different owners, but it is usually for a safe place or something to travel in... not a time-out place...
2. How big should the crate be? this is a cat crate. I could probably fit 3 sleeping Rex's in it but no more- is that too small- or is small good?
A bigger crate for a smaller dog is not a good idea, the right size would be the same size as your dog, like say your dog is medium, buy a medium sized kennel... not a large...
3. should I be closing the door to get him used to that- or will that make it negative?
Sometimes the closing of the door scares the dog, if your dog is in the kennel and seems used to it, try the closed door... then give your dog a treat to show him that your happy with that behaviour.
4. Should he be staying in it all the time at night or when we are out or is being kept in the secure kitchen better
Being kept in the secure kitchen is (IN MY OPINION) better, but some owners disagree and would say put your dog in the kennel, so I have no idea....
Good luck