when I will create some game with many levels, is it better to have my project like this:
1 level = 1st layout
2 level = 2nd layout
3 level = 3rd layout
or like this:
1 level = 1st layer
2 level = 2nd layer (the previous one would be invisible)
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If you search, you'll find that Ashley has answered this previously.
Layers are meant to be combined in a Layout, where each Layout would represent a Level. The Layers would be used for such as Parallax, Hud etc to add detail to each Layout/Level.
It's the best and most logical way of doing things.