My question is do I have to make a seperate layer to shade limbs of my stickfigure in flash? Because whenever I use line tool, make my character, and then shade limbs the darker limbs come out on top in the preview.

Yes.
Same goes for brush tool.

What you can do is set your line to object drawing. Then you select the line and press ctrl+shift+down and the line is sent to the back.

Oh sweet thx both of you