So what do I do? I try my hardest not to get conditioner on my scalp. Conditioner is for the hair, not the scalp so I apply it mid length down. Then when it is time to rinse it out, if I've used a thick creamy conditioner, I like to use a co-wash conditioner to ensure that my scalp is product free. As a treat for your scalp you might also want to consider doing a baking soda scrub. It's really simple, all you do is mix baking soda with water to make a paste and then use it as a mild exfoliant on your scalp. It's simple, natural, and it works well.
Flaky Scalp Fix
I absolutely love deep conditioning my hair, there is something very relaxing about taking my time, ensuring that each strand of hair is thoroughly coated in conditioner, and then leaving it on overnight for deep penetration. But I've come to realize that a simple rinse of the conditioner is not good enough to make sure it has all been removed from my scalp. Just rinsing, regardless of the length of time I spend rinsing does not remove all the conditioner from my scalp and the end result is flakes. Once the conditioner dries up, it can cause itching and flaking. So, while you might think it's dandruff it's actually dried up conditioner.