Hi, Brynn!
Thanks for joining in on the conversation.
It does sound like everything is set up correctly on Shopify’s end, considering you’re only seeing one pixel in the Pixel Helper, and you’ve only added the pixel in Preferences, rather than in your theme’s code.
I did notice that you mentioned KIT, however, and this could have something to do with seeing multiple pixels on Facebook’s end. Our Support team will be able to verify if the extra pixel is coming from KIT, so feel free to contact us and we can investigate. Our Support team will also be able to determine if any of those extra pixels are associated with Shopify.
As for your catalogs, the Shopify Product Catalog would be the one that was created if you had migrated over to the new Facebook channel from the old Facebook Shop channel (which has since been delisted). This product catalog should not be deleted, otherwise you will lose the sync between Shopify and Facebook.
I hope this helps clear things up but feel free to reach out should you like us to take a deeper look!