Hey there Vanessa, (Warning - this post is LONG- Sorry in advance!)
I am also a new owner of a Yorkie pup.. though mine is almost 5 months, named Toby.
I know there's a LOT of info out there and it can get contradictory and very confusing. When that happens, I trust my gut. This is your dog, and use your intuition to decide what's right for you and your dog. (of course this is only my opinion)
re: crate training
Personally, I have never used a crate, but it comes highly recommended by the pet stores/vets/books...etc. Things are fine without it. He has a bed and his own "space" to go to when he feels anxious or nervous. I haven't bought a crate cause I just don't have the space for it right now...
re: the food
When I brought Toby home, he didn't eat much for the first few days.
He was VERY excited and we didn't sleep much the first few nights.
We are feeding him the same food he was fed before
He seemed to start eating on the third day or so once he got a bit more settled into the new surroundings.
I have purchased an online book for Yorkie's and in the .pdf document it states that these particular dogs shouldn't be fed wet food. Perhaps it's wrong, but I find that it's better NOT to feed them any kind of food that's found in a local grocery store - it's cheap and filled with fillers and/or animal byproducts (EWWW!)
You should ask the vet for a good food for your dog - he/she will know best.
Invest in Puppy vitamins!! These are really ultra helpful to ensure your dog is getting all the essential nutrients & vitamins a growing puppy needs.
I've been using Excel daily supplement... it seems to be tasty (?)
I only use a really small amount (pea sized) 2x a day.
re: leaving your dog alone for long periods/seperation anxiety
I'd say in my opinion, that again, this is your choice to make. For us, we let Toby stay in an area of the apartment, but block off places that we don't want him in. For me, I wouldn't want to leave my dog in such a small area for a long period of time, esp. near a wee pad. It's just not that sanitary for them... and your dog may end up smelling like the wee pad.. ? just a guess here ? If you go with a "designated area" make sure that if they pee or poo on the floor (somewhere other than the pad) then it'll be easy to clean up.
Also don't leave things on the floor that can be eaten or chewed up.
I've heard that these dogs are really people lovers & don't like to be left alone (that probably goes for all dogs), but I'm sure that your dog will adjust soon. My best advice here would be to try to start leaving your dog for short periods of time, and gradually work up to the long periods. This way the dog will be less traumatized when it's been left for over 6 hours long.
I understand you have to go back to work on a certain day, but perhaps you can start leaving the dog alone for longer and longer periods before you go back to work. It will just ease them into it more.
As for the whining/crying....
Personally I would feel terrible to leave the dog in the cage at night.
My friend has done that in the beginning and now has stopped doing it.
She puts her dog's bed right next to hers and things are fine.
My dog's bed is right next to mine (with a baby gate) and pee pad.
We've been having good nights and things are running smoothly.
Your dog may appreciate this if you let them sleep outside of the crate (again this is JUST my own opinion) and may start to eat and play more and more.
Sorry for the LONG drawn out Post!
These are just my own opinions, I think the best advice is your own GUT along with information that feels right.
All the best of Luck!
Post some pictures when you have some time
Thanks for letting ramble sooo long!
Molly & Toby