Whether it's from your battles against acne, from a peel, or just plain dehydrated skin...flakiness is annoying AF! While there's no way to fully hide flakiness using makeup (I'd actually recommend trying to adjust your skincare routine to minimize the flakes), there are some things you can do to stay looking your best.
1. Stay away from matte foundations & powder. Anything that is inherently drying or used to help control shine on the skin will definitely make flakiness worse. I'd recommend skipping powder in any areas where you are flaking, and instead opt for a makeup setting spray like this one to set your makeup. Something you might want to consider is swapping to a dewy foundation, or at least using one that has a silicone base. Silicone will help glide over the dry spots, and anything dewy or moist will be beneficial for this as well.
2. Pat on your makeup. Instead of doing downward strokes with a foundation brush or sponge, I'd highly recommend you use a patting motion instead. Patting with a beauty sponge like this one from June & Co will help press the flakes down a bit, whereas dragging a brush or sponge across them can kind of 'kick them up' so to speak.
3. Resist the urge to pick. This isn't really a makeup tip...it's just a friendly reminder. You can use gentle exfoliating products (like an enzyme mask or something of that sort) to help lift off the dead skin in a way that will actually help reduce the problem...picking at them won't do you any good and will only irritate the area further.
4. Use creamier products. Along the lines of switching to a dewier foundation, you might wanna go a step further and use cream blush, cream bronzer, liquid highlighter, etc. Using moist products wherever your dry skin appears will not only make things easier to apply, it'll also make sure your makeup isn't making things worse.