The best thing to do is to set it up exactly like the template files. If you start with the Chloe template and just replace the layers with your own (keeping the naming structure and order intact.
however, as you have already created it, use this screenshot as a guide on how to arrange and set up your layers. Notice specifically the Crowns, make sure you have a crown on the character group and the other independent groups such as arms and facial features , as in the illustration.
1. You did the right thing removing independence from the Body group. Now select the Body group (not the Body BG layer) and add the fixed handle(s) there and it should stick.
2. For the hair, see how Cassandra is set up at http://okaysamurai.com/puppets/ - should give you a good example of how to add background hair.
3. For the arms, you have to decide if you want them to be in front or behind the torso. If you didn't want the bust overlap you could either a) cut out the overlapping parts, or b) make the bust layer above the arms so they appear behind it.
Comming back with another question. I looked at the bussiness lady with the coffe cup but it didint really help me. When I include her staff it pulls on her face or her arm doesnt move with it. I needs to be above the hair and face so it wont be hidden by those things. Any suggestion. The hand that holds the staff and the hand are both in the staff folder.
If I have it in it's own folder away from the main character folder then it does this.
Hand is detached
Here's my tree.
Like before, you kinda have to pick now if you want the hands (and anything associated with them) in the front of back of the character. Currently there's not a great way to attach things outside of the head and body.
The best thing I can think of is something like the guitar setup here where the hand and arm for the guitar neck are separate layers and the guitar is sandwiched between - you might be able to do that with the rest of the character, not sure.