Congrats on your new addition and welcome! This is such a great site and FULL of great info and helpful people.
I have a 12 week old myself and went through a lot of what you're going through right at first... It's mostly first-time parent nervousness I think!
Just wanted to share with you a little of what I've learned so far:
Kennel cough... Lily has it right now.
It sounds like a dry, honking cough and then a gag at the end. If your baby just sounds a little phleghmy, that's probably not what you have. HOPEFULLY you won't have to go through this too!!
My little one doesn't wear a collar... I've read a lot on here about people not putting collars on tiny dogs b/c it's not good for their throats. Is it a flea collar by any chance?
Lily eats about 1/2 a cup of dry food a day right now, but for the first couple weeks, she only ate MAYBE a 1/4 cup daily. You need to invest in a good quality food since Yorkies can have allergies. We feed Wellness. I've heard lots of cons against feeding Science Diet, but like our aunt/vet told us: some dogs do really well with it, but there's a lot of dogs that don't. Also if your baby is really little, it could be that she's not eating the dry food b/c her teeth haven't fully come in. Wet it with some warm water, let it soak 10 minutes or so and then see if that helps.
I know a lot of people don't want to let their babies go outside too much, but we take Lily out for 15-20 minutes at a time to play a little and get some fresh air.
We crate train too, and I take Lily straight outside (don't even let her feet hit the floor) if she's been crated or sleeping for ANY amount of time, even if it's just 10 minutes. That's helping to get her in a good pattern of only going potty outside. Try small amounts of time in the crate at first, and then PRAISE PRAISE PRAISE when she goes outside. We reward Lily with Cheerios... she's a food motivated girl.
Hope all this helps!! I know it's long! Good luck and best wishes!