I sell nail stickers and with every order, I send free nail file/cuticle stick in a little baggie, and an instructional card for how to apply them. I want to add two features in the checkout process:
Is there a way to do this? Ideally it will auto-populate during checkout and they can either remove it from the cart or add quantity or a note.
If you're on Shopify Plus you might be able to do this. If not, you'll have to do it within the theme code, either in the product or cart pages.
I'd recommend the free gift as an opt-in, rather than an opt-out. Then put a check box (and quantity selector if you want) on the product page where they can add that item to cart. From the development side, you can use the Shopify ajax API to programmatically add the free item to the cart.