1. I have a wood floors and it seems a little slippery for my puppies, especially when they get excited. Is this safe? I see them slip here and there while playing with each other and I'm afraid that they will break a bone or something. I also can't carpet the whole apartment so I'm not sure what my options are. I do have a carpet that covers 1/4 of the apartment.
I'm not really sure about this, I've always been concerned too. I play fetch with Jackson down our long hallway of wooded floor and he slips and slides alot. But he's never had a problem thus far.
3. I also have a 5-year-old yorkie that's currently at my mom's house. When I was raising him I made available solid gold wee bit kibbles 24/7 and there was no problem in raising him into an healthy adult. However, I do see a lot of suggestions on here saying that the owner should feed them twice a day, etc, and no suggestion of leaving it out throughout the day. Is there a specific (unhealthy) reason why? I just refill both water and food and it has worked out fine in the past.
I think it just depends. Some dogs free-feed very well, others will gorge, and others won't eat enough. It's often recommended to leave food out for puppies all the time so they can always have access to food. But it's all a matter of preference and your lifestyle, etc. I tend to put the measured amount of food in Jackson's bowl in the morning and whatever he doesn't eat by dinner gets mixed in with wet food for his dinner meal.
4. I just went to a vet for first time check up and the bill came out to $450 for both two healthy puppies in NYC. 
The checkup included first set of vaccinations and stool sample testing. I don't recall what I received with my first yorkie bc it's been so long, but I just wanted to know if that is normal. Also, the vet recommended getting the rabies shot after 12 weeks, is this true?
That sounds about right, especially for NYC. I remember Jackson's 12 week appt. being about $200 or something along those lines, because they charge new patient fees, and all that stuff, plus the vaccines, etc. You should hold off on rabies as long as you can legally, IMO. I think most states are about 4 months old but I'm not entirely sure.
5. Lastly, I'm planning on getting them microchipped. The vet says it is $70 and I'm wondering if it's reasonable. Also, is there annual fees I should be aware of? How old do my puppies have to be in order to get them?
Jackson was microchipped for $25. It's probably best to do this when they get neutered, because the needle is pretty big. But I've read some do it when they are not under anesthetic and do fine.
