Puppy should certainly have a bed in the crate and you can put something in that will mimic the rhythm of a heartbeat to comfort puppy if you find it necessary.
I covered the top, back and sides of my puppies crate to create a cave like feeling which can help to make a puppy feel secure.
Also take the puppy's collar off when in the crate as they can get caught on the bars.
I take it you're talking about overnight and as you will have to let it out during the night for wee/poo you could offer water then if you don't want to put water in the crate, although dogs really should always have water available.
And you'll probably find that puppy won't want to be left alone for several nights so you night find yourself sleeping near the crate or having it in your bedroom overnight for a while, if you're willing to do that.
As regard new puppies going in the garden, mine had been going in the garden at the breeders house (she'd fenced off a little part near her back door and would put puppies out regularly as soon as they were old enough) so I just continued to do the same.
Some people use puppy pads but then you have to retrain the dog to go from the puppy pads to the garden; easier just to go straight to the garden.