Welcome to Yorkie Talk and congratulations on your new pup!
The biggest red flag relative to the breeder is that she/he sold a Yorkie as a "golden merle." There is no such designation in the Yorkie breed standard set by the Yorkie Club of America and recognized by AKC.
Some unscrupulous breeders will use terms like "golden merle" as a marketing gimmick to charge higher prices or to cover for the pup not being full Yorkie.
Regarding vaccinations and health, get to a vet immediately for a wellness exam and set up a schedule for the remaining puppy vaccinations. Hold off on rabies until about 6 months. Read the vaccination threads in the library in this forum to choose which vaccinations you want for your pup.
For potty training, I would put another pad just outside the pen for when your pup is roaming free. Don't let him have run of the house though. Keep him in the same room as the pad while he is small and training. Puppies tend to not want to travel long distances or expend too much energy getting back to the pad. Their little bladders often won't enable them. Plus, they often don't want to leave the scene of action or their humans to go to the pad.
Although you are going to also work on pottying outdoors when you are home, I would also allow him to keep the pad at all times. My boys have the pad all of the time and we go outdoors as much as possible. Don't have the pad disappear while you are home. That will be confusing.
Biting: Pups under 12 weeks who leave their litters/moms tend to be more prone to biting. Usually the mom corrects them and teaches them not to play so rough. Teething is another factor for the first 6 months or so. Say "no bite" and take away your hands or whatever other targets he is going for. You can also yelp like a dog when he bites you.
Crying: is this mainly at night or when you have to leave him? He is very, very young. Puppies tend to do that and Yorkies especially want to be with their humans. Try giving him a tshirt that you have worn. They love clothes and things with your scent. I've always kept my boys in my bedroom with me at night and that relaxes them.