can i take my medications and my daily supplements out of their regular bottles and put them into smaller bottles or plastic sandwich bags.

I wouldn't, original bottles are better to prevent any confusion.

Yes just write what they are on the bag

TSA rules want you to keep your meds in their original pharmacy bottle. What I do is put all my meds in their original bottles in a large ziploc in my carry on. Same for cosmetics and perfumes, lotions, shampoos, toothpaste (which have to be 4 ounces or less). Hope this helps. Have a great trip!