There are 2 things you need to enable to ensure your cart upsell shows on your store.
1. Make sure your cart status is set to "Enabled"
2. Make sure you have activate the Atlas Cart Upsell app embed in your themes settings.
You can do this by clicking the activate button in the cart upsell app which will do this for you. Or you can go into your theme settings in app embeds and toggle the Atlas cart upsell to on.