Welcome to YT.
You're certainly correct that they are like having a new-born. In fact, having a yorkie is like having a baby in the house all of their lives. They never really grow up.
The guilt will probably never leave you. I have always felt guilty, even while leaving mine for a a short time. It's part of having a yorkie in the family.
I think it's wonderful that you plan to take her to Doggie Day Care when she's had all of her shots. The best thing you can do for her is to ensure she is well-socialized in all sorts of situations and all ages of people. A puppy that is well-socialized at an early age will be happier and well-adjusted.
She cries when you are home and she is in her playpen, because she is separated from her pack. She has already bonded to you and considers you and her a pack. She just wants to be with you all of the time. That is a typical yorkie. A yorkie will follow you wherever you go in the house.
It will be easier for you when she is fully housebroken and is allowed to have free roam of your apartment. It will probably take longer to get her housebroken since you work, so don't become frustrated and don't ever give up hope. Just be very diligent and very consistent in your training. When you are home, spend your time playing and training her. Give her your best and she'll give you her best. Don't think that you made a mistake getting her. You didn't. Things will work out. You'll be the best of friends forever! Whenever you have any problems, just ask someone on YT and you'll get plenty of opinions to help you find a solution.
In the meantime, be sure to use only an enzymatic cleaner on those spots. This link will give you some very good information:
Removing Pet Stains and Odors : The Humane Society of the United States