Layer visibility setting is completely ignored for rendering.

Layer order is Start at bottom to End at top.

Layer pane
    1st layer to draw is BOTTOM one in Layers dialog.
    Cannot have "no" or 0 duration on any frame.  Either default duration or
     specd.
    Specified duration is just a suffix in the layer name:  (100ms).
     Value must be > 4 (apparently rounds down 5 millis (modulus 5)).
     NO SPACES WITHIN THE PARENTHESES!!!  If you have spaces, the setting will
     silently be ignored!
    Duration is how long that frame will show up.

Before writing GIF
    <Image> Filters / Animation / Optimize (for GIF)
     (Changes framing from replace mode to combine mode)

WHEN writing GIF  (this probably useless, as described)
    <Image> Image / Mode / Indexed [Do not do beforehand, or your palette will
     be constrained.
    I see no diff as long as you "Optimize (for GIF)" before saving.

TRANSPARENCY
    Without optimization, transparency works fine as long as export with
     Frame-Replace mode.
    If do not use Frame-Replace mode, OR if optimize, previous frames will
     bleed through transparent areas of current frame.
    Therefore, basic strategy is to
        Use transparent layers for mobile objects, so can see multiple layers
         at once.
        Leave no transparency in final animation frames.  (Probably makes no
         diff if there is a transparency channel).  Delay the merge-down of
         previous item as late as possible.
        Optimize Gif and Save Copy As from this temporary image.