Regarding the crate training (I have never crate trained before), I will/ should remove the pen and set it up at another location. Then, leave the crate door open? Yes, leave the door open so he will become comfortable going in and out of the crate. When you want to crate him, put a treat or piece of meat in the back of the crate to entice him to enter. Once he enters, praise him and close the door.
How often did you want to crate him during the day? How long?
1) the pup would definitely not going in unless I feed him there. Should I close the door immediately? Yes
2) I could lure/motivate the put into crate. How long should I keep him there? I understand that it should be brief and extend the length periodically. Keep the pup in the crate for as long as you want to crate him. For example, if you want to leave the house to run errands or go to work.
3) should I leave the pup there and move to another room or sit next to him? Where is the crate? The crate should be in a area close to the family.
4) When not in crate, where should the pup be doing? Wandering around on-leash? Allow the pup to check out the house and move about freely. Keep on leash while he's learning to accept the leash or when guests come into the house. Do you have small children in the home? If so, leash the pup when they are playing. Do not allow small children on the the floor with the pup because he will think they are playmates. Puppies play by biting, nipping, growling and barking.
5) I bought him a crate that has divider and it is a very comfortable size, not too big that he can potty but not to small that he can't stretch. Definitely, can't put his water bowl in their. So, if the water is not in the crate, does that mean that he should not be in the crate for long period of time? (right now the water bowl is in the pen and he sleeps near the water) Do you allow him to potty in the crate? He should be trained to potty outside only, not in the crate and not on pee pads.
If you cannot put water in his crate, then "no", he should not be in the crate for long periods of time. Pups at all ages should have access to clean water at all times.
Hope that helps.