The simple answer to the arm thing is either to place it under your leg layers in the layers list or adjust the “z level” param. That allows you to move things up and down on the canvas while keeping them in place.
It might help you out to look at the post I made here and download the “paperdoll” file. All you need do is plug in whatever you want the character to look like… well, have a look, I bet there are a few things you might find useful (including where I put arm layers!).
M