If your image is meant to be a full-blown scene with characters and background, then it’s very important to plan it that way, doing thumbnail sketches/color studies to work out all of your visual design problems first, as simplified versions of your finished image, with just basic shapes, values, and colors. The mistake that too many inexperienced artists make is to jump into a full sized image with lots of details without having done any planning at all, and just start to arbitrarily add stuff to it. That’s like shooting a movie without a screenplay, or performing a piece of music without having composed it first. Serendipity might give you a few pleasant surprises here and there, but overwhelmingly, lack of a plan will have dire negative consequences in your work.
1,000 layers is absolutely overkill and unnecessary, taxing your computer’s resources, slowing down the workflow, and a nightmare to manage. There are far more efficient workflows and management methods–ones used by experienced professional artists. The most important thing you want to keep in mind when managing your layers, is that anything that could be repainted fairly fast and don’t need to be isolated for random, sudden changes in value/color/size, do not need to be meticulously kept on separate layers. What you need to keep on separate layers, are the shapes and objects and characters that might require random and sudden changes as you move them around, resize them, change their values/colors, etc, as well as elements that would be too much work to separate from other elements via lasso/magnet selection (for example, hair, with all those detailed strands). At the basic level, you just need to keep your characters separated on layers from the background, as well as any background shapes overlapping other background shapes (such as buildings that are closer or further back at different Z-depth planes).
Doing monochromatic versions first and then colorize later has its advantages, but it also has its drawbacks. For example, any kind of minute detail you do, you’ll have to carefully redo them later on the color layer to match, and that’s unnecessarily doing twice the work. If you do effective planning in your thumbnail sketch/color study stage, you’d have figure out all those problems early on and don’t need to do a monochromatic version first. Also, even if you work full color right away, you can still add colorize layers later and completely change the colors if you want to, so you’re not missing out on anything by going full color right away. Some people work with monochromatic versions first because they don’t want to be distracted by colors, but I think that’s just avoiding learning to work in color properly, and one of the things I really train my students to learn, is to develop the ability to not be fooled by the deceptive values of colors, so they can make color judgments effectively and not be afraid of it. I have very challenging exercises I have them do to force their brains to split all color information from value information and deal with both simultaneously, and still nail the correct chroma they are aiming for. This is extremely difficult for some students, but with my guidance, they almost always end up getting it right.
My suggestion for this piece, is that do hold off on going any further and do some thumbnail sketches and color studies first, of the full scene as you see in your head, with the characters and the background, and work out all the visual design issues like composition, value management, colors, lighting, etc. They can be quite simple–something like the color keys we see in the “art of XXX” books from Pixar. If you don’t know what they look like, just google for “pixar color keys” That’s pretty much the golden standard for clearly readable ye simple thumbnail planning that works out all the visual design problems, without going into any details.