When my daughter was a toddler and going to daycare, she had tops and bottoms that went together. Whenever her dad would dress her, he just grabbed anything. I began folding her clothing with pants on the bottom and shirt on top with underwear and socks sandwiched in between. I pulled out a set the night before and sat it on top of her dresser if he was the one to dress her in the mornings. It worked like a charm.
Later, in grade school, I would still fold and match pants with tops in the dresser, so she could just pull out a set and know she was matched up. Now that she's in high school, we just go with pants in one drawer and tops in another. Her wardrobe is primarily black (a phase I can live with), so there's no problem coordinating. If she does a burst of color, she usually runs it by me, but she really does a nice job on her own. I tend to only buy things that coordinate and when we buy separate pieces, we talk about how they pair up with other things to make an outfit, so I'm sure that helps.