yeah the handling of layers across frames leaves something to be desired for sure. better to settle the amount of layers before you add any frames. you can drag&drop a layer from the layers area to the frames area though and it'll copy just fine.
the second color is what you select with the right click, like you said it has a diagonal line over it. it's function is just pretty much that's what you erease to when you select "fill selection with second color" under file/preferences/tool
Also, if you want to make a gradient left click on the first color of the gradient, then right click on the second color and select "make gradiation.." it's pretty handy.
I know you're used to having the background replaced with transparent when you move a selection, but imagine you're rotating a face, or slightly extending a limb by one pixel, you would want to just drag the part that moves by one pixel and leave what's behind it unchanged. You can enable it by going to file/preferences/tool and checking "does not erease image under selection". it functions pretty much as if whenever you drag something you had copy/pasted it. too bad you have to go to preferences to enable/disable it, a hotkey would be sooo much better