Seem like your puppy is just going through the normal stages of bonding and testing you limits.
Fist I suggest you get a small crate. Then as the other suggested put a t- shirt or something soft in there with your scent...next
bring the creat upstairs with you at night and place beside your bed...
if he starts to cry... tap on the top of the crate and say quiet.
when you turn of the lights to go to sleep say something like (bed time.. )
he won't know what it means now.. but he will get the hang of it.. ( that now it time to sleep and be quiet.)
What every you do not take him out of his crat unless it is to potty.
Then he will still keep crying. Thinking you will let him out.
When he get better and stops crying at night ,then you can slowly start moving his crate to the location you want him to sleep in.
For the first few weeks it is really hard but it does get better