Here's our practice that we've learned after 40 years and 3 dogs. We crate train for night time and use a different carrier for travel that requires confinement. We found using the night time crate for travel confused our pups. For our yorkie, her night time crate is in our bedroom on a hamper so she's at the height of our bed. She goes to bed when we do and gets up when we do - or sometimes we get up when she does. lol In her crate she has a dog bed that fits and a small blanket. Before bed we have a routine where she goes potty, has a tiny treat, and goes to bed. When she was very young she wore a little cotton jammie because she didn't retain body heat very well. Now that she's older and has longer, thicker hair the jammies can make her sweat. So not more jammies. There is a night light in the room as we learned our pup is afraid of the dark!
During the day we have a little pen that is larger and see through. Inside is a throw rug, a dog bed (which happens to be like her other) and a larger blanket, a nylabone, and a non-stuffing toy. Her food and water are always in there, too. We do not put her pee pad in there as you don't want your dog to soil their food/sleeping area. Before we leave, we take her potty and put her in her pen with a little treat, close the gate, and confidently tell her we'll be back soon. Sometimes we will leave the tv on or play some soothing music. We always leave a light on as our pup (we learned) is afraid of the dark so if for any reason our return is after dark or delayed she's got light.
We also have a matching bed for her in the room where we watch TV. She loves to be with us but sometimes if we're up and down too much and she just wants to chill, she'll lay in her tv bed.
Our pup is pee pad trained. We use a silicone mat with the disposable pee pad on top that is tucked in an out of the way place that she can always access unless she's in her pen or crated. We change it routinely every morning and wrap it in a grocery sack before putting it in the trash. We always pick up poop immediately with tissue and flush it. If we are having company we change it before they arrive
no matter time of day. lol We are very sensitive to becoming "nose blind" so her beds, blankets, etc. are washed regularly and her pee pad area disinfected so our house doesn't smell of dirty dog, just clean dog.
This process of night training takes patience and perseverance. Her crate started within arms reach and if she cried I would just reassure her and let her smell my fingers through the door. If she seemed frantic, we would take her to her pee pad, and then right back to bed. It took a couple of weeks of consistency. Then we slowly moved the crate back to where we want it inches at a time. The lifelong rewards for you and your pup will be great by investing effort now to create a bond through confident training. Be sure to learn daily grooming, too. It's part of the bonding process as your pup will gain confidence in you to care for her every need.
Enjoy!!!!