Young puppies can go hypoglycemic very fast and it can kill them, I know from rescuing my Gizmo, who was in a hypoglycemic coma when I went to rescue him. He was being starved and the vet did not think he would make it through the night. Thankfully with a lot of time, love, and nutrients, I was able to get him through it, and he's a healthy 4 lbs now at 6 months. Gizmo was 1 lb 4 Ozs when I rescued him at 9 weeks, and it sounds like your pup is very small too. I would give him nutrical a couple times a day to make sure he's getting the nutrients he's eating. I also hand fed Gizmo when he did not want to eat and this worked amazing, you would be amazed at how much a little hand feeding can do. I kind of switch up his food when he seems to get tred of it. I go between royal canine yorkie and the wellness brand, and he eats really well. Another thing is at that young age I would allow him to free feed because he's so little, and the calories probably don't last long in his tiny tummy. I also will mix different things in with his kibble to make it more interesting to him, such as a little bit of cottage cheese or vanilla yobaby yogurt. The calcium from them is good for their bones and stuff as they grow :-) a lot of times all it takes is just warm water mixed in :-) I would not worry about getting him on a feeding schedule at that young of an age as they really need the calories and nutrients so their blood sugar does not crash. Gizmo has now got himself into a schedule of eating 2 to 3 meals a day, and he just did this on his own. Over time, he stopped eating in the middle of the night and in between breakfast and dinner, of course except his few treats he gets during the day lol.
I also have an xpen for Gizmo with plenty of room for his peepad, water and food, as well as his bed and blanket, and several toys to play with. I have the richell xpen which is really nice and it expands as they grow. It also has a tray underneath so you can put it anywhere without worrying about your floors :-) here is a link to it
Expandable Pet Pen Medium w/Floor Tray , what is nice also with this pen, besides being super well built, is you can buy a expandable top as well, as yorkies become really great climbers, and that will keep him safe while he is alone, yet still give him plenty of room :-) I put only half the top on at night so I can drape a sheet over the end where his bed is to make his sleeping area like a den, which calms puppies very well at bedtime. I only tred putting Gizmo in a crate one time, and he was so scared I never put him in there again. I think it was because he came from a back yard breeder who kept them in cages. Once he had his xpen, he never cried about it again.
As for the aggression, I have two grand daughters, and when they are over I let them be the ones that reward him for doing good behaviors such as using his potty pad and such, they will give him little treats. I also let them walk him and play fetch with him. Basically I have him associate them with good and fun things, and he does not see them as a threat, but rather as something positive, as its probably just fear reaction from your pup, but instead, he sees them as the ones that good things will come from. I can see it has worked well because he gets so excited when they come over and can't kiss them enough :-)