The 'square' thing is a masking layer. Im not sure what teminology your Photoshop uses for it. Im not sure it you "Insert, Layer, Mask" or whatever.
The problem you are having with the line on the panel is that your using a Panel Layer that was merged with a layer that contained just an 'outline' for the panel. Normally, you'd have two layers, one for the panel and one for those two lines (which are what I would call an outline for the panel).
If you want want the 'lines', I would use the magic wand tool to try and delete them from your Layer.
On a different note, I always remote the checkbox from "auto select layer". I hate it when Im working on a layer 'underneath' another layer and the damn application keeps selecting the top layer when I click.
