I use shallow/deep drawer organizers from The Container Store (they run maybe $3-6 each). For some brands, I may store laying down, but generally, I like to store them standing up. I organize by both brand and tier, depending on how many I have within a brand.
I try to plan out 3-4 looks at most, and I’ll usually try to coordinate and overlap colors so I can bring less. I do the same with lip and blush colors, too. For lips, I try to bring one light and one dark shade, so if I need something in the middle, I can mix. For blush, I usually pick one warm and one cooler shade.