SO, you took off several days to be with your new puppy....
I'd say that's a VERY lucky puppy !
It's hard to leave them alone, but, many people do, and the animals deal with it pretty well, after they are adjusted to your schedule.
She wants to be with you when you're there, that's why she crys, and you can do that (leave her out of her pen) it's just getting used to "keeping an eye" on her, it's not that hard once you get used to it.
Be sure you get some Naturalizing Spray for those potty "spots", where you can keep up with eliminating the possible areas, getting her to focus on one area for that. She just doesn't know now, but in time, will want to be clean and do it in the right place.
It's nice that you want to Socialize her, a couple days at Day Care sure will help, but... that's up to you. Many do not do that (me for instance). I'm not all that concerned that either of mine is "socialized" like other dogs. I'm perfectly happy with them being a little "aloof" toward other people and other dogs as well. That doesn't mean that they are aggressively going to bite the Vet or Groomer, it just puts a little distance between people and animals we don't know, and our little ones.
If other people don't like it....TOUGH !
It sounds like you're going to be a GREAT provider for your little pup,
be patient... it's SO rewarding !
Have a good Day !
S.W.