Hello everyone. I'm a new Yorkie mom and I've been looking through all the forums here for a few weeks now, but I need some advice. My Yorkie, Alice, is 5 1/2 months old and I've had her for about 1 month now. I got her from a "backyard breeder" who works with a relative of mine. She was free because it was an accidental litter and they couldn't get their tails docked. but I saw the whole litter and the parents and they were all happy, healthy and clean so I brought her home. She's a happy puppy and super sweet but kind of skittish and extremely submissive. She bonded with me within the first 24 hours and prefers me to anyone else. She follows me around the house even if she's in a dead sleep when I walk into another room, she still follows. She loves nothing more that to cuddle on my lap and I love it too, it's definitely different than what I'm used to though. I have her sleep in her crate in my bedroom (hubby won't let her in the bed lol) and it only took a few days of her whining for only the first few minutes to sleep quietly in the crate all night long. Housebreaking and pee pad training is progressing well.
The problem I'm having is with all training in every other area. We also have an old beagle and an Akita and this is my first experience with a toy breed or a terrier. Simple things like, sit, down, stay, come etc. were so easy with the other dogs (even the Akita who are notorious for not really caring much about their owners' agenda lol). Alice is slightly encouraged by treats, but not to the extent that I'm used to (the dog willing to do ANYTHING for the treat). Praise doesn't really work too well with her while I'm trying to teach her because she always seems to be scared when I start asking her to do something i.e. gently push her hind end down for "sit". She gets petrified when I apply even the slightest pressure on the leash (but she will walk around the house with it attached to her collar if no one's holding it) even if I'm holding a piece of cheese in front of her and sweetly calling her forward, she'll only reach her head forward for it. I don't want to pick her up and try to sooth her in these moments because that will reinforce the nervous behavior. I'm trying patiently but she doesn't does seem to be getting any of it (my other dogs learned "sit" in like 5 minutes). I really like my dogs to know commands, like our Akita will go into her kennel if I say "house" and they will both walk away (like when we're eating) if we just snap our fingers and point to another area of the room and we didn't even really "teach" them these things, they just respond to our body language and "energy" (yes, I'm a Cesar Millan fan
The basic gist of my question is; are Yorkies hard to train, does it take longer, is there something that I should be doing differently with this tiny dog than I did with my Beagle and Akita? We used a "puppy class" at a local dog training club for the Akita but she responded so much differently to training and people in general than my Yorkie is. Alice just gets scared really easily whenever something or someone different is introduced to her (she shakes and will either try to bury her face into me or hide) Also, even though she now is really comfortable in our house and me and with places she visits often like my mom's and grandmother's house, she will still most of the time run away from even ME or cower when I go to pick her up, even if I go slowly. She is very playful and is always either running around our house like lightning, laying on my lap, or playing with her toys or our cat. I just can't figure out why when I sit on the floor with a piece of cheese and call her to me or put a leash on her or pick her up off the ground she gets scared??? I'm sooo not used to a dog this small (at almost 6 months she's only 4 pounds). She ran away from me in our yard today while sniffing at the ground (it's not fenced in but the only place she can really go unless she ran really far is one of our neighbors yards) and I couldn't catch her or get her to come to me no matter what I did until finally she gave up and cowered on the ground. Our other 2 dogs get attached to a 10 foot "tieout" that's attached to our deck which is what I what I was planning on eventually doing with Alice, so obviously she needs to accept being on a leash and learn to come when I call.
I've establish a strong bond and trust with my new little furbaby and I'm gentle and super affectionate with her while still making her fit into our "pack" with myself, my husband and our son as the "alphas". She has fallen in line with the other 2 dogs for basic everyday routine and seems to really love her new home here yet I'm having such a hard time teaching this dog just the basics. Sorry I'm so long winded, just want to make it clear about her personality, my usual philosophy for "dog psychology" and training and what the specific problems are. I appreciate any advice greatly

Oh, and yes, she has seen the vet twice so far and has a perfect clean bill of health