I like your sprite so far. You need higher contrast between colors, especially in the helmet cause your black, dark blue and gray are to similar, so it's hard to read. Those brown spots on the legs are not symmetrical, one is on the side of his right leg and second one is almost on the front of his left leg. By removing second one you will still preserve concept detail, and you'll solve the problem.
About layers, as rikfuzz said it's not a problem if you don't use different opacity layer which will generate additional colors (again this can be tweaked in final image so it's not so big problem). If it helps you use it, people use it for animations regularly.