I use boxes like this to keep napkins from stores from being all over the place. These boxes are also great for keeping travel sized pouches of disinfectant wipes in so that they stay moist. Then I put other items like headphones, headphone splitters, eyeglass wipes, etc in small soapboxes like this. For larger items you don't want banging around in your car, I suggest shoe boxes like these.
I have two medium sized Caboodles cases in my car at all times. In one, I keep a few doses of all my medications no matter the time of day or night I take them. I also keep over-the-counter pain relievers, eyedrops, extra contact lenses, antacids, band-aids and anything else my family might need for first aid. In the other case, I keep duplicates of all of my makeup. I have this exact case. There are little compartments and elastic bands to hold brushes and small items. This way I’m able to get dolled up at anytime. If you need to organize even more within the cases, small cosmetic pouches are great.
I recommend clear for all of the organizers because it's much easier to see what's inside at a glance. I hope this helps you tame the clutter in your care.