My Rough Layouts (which sometimes has many layers/folders) are in a folder that I tend to color layer red.
Having my Layouts in a folder helps when I want to try out something different-- just duplicate the folder.
Here's a page that went through 6 versions. (note how V2-- V5 are color layered RED).

Then either do my pencils above the roughs, then place them in folders according to the panels OR use my Frame Folder Tool to make the panel layer masks/folders and pencil in there.
When I am ready to ink, I always turn the layer below, whether Pencil or Roughs to a color layer Red.
I also take advantage of coloring my layers so I can easily see what layer I'm on or know which layers to turn back on or off (I don't do this for every page, only when needed)... tho I am using it a bit more lately... In this case, green is go/good, yellow was reworking.

Here is a sample Panel that has a character.
The Blue Ink color layer was the original and I duplicated it to change some art around, that is why layers say COPY. You can also see my Rough/Pencil Reds on the bottom turned off.
