We don't recommend you to connect multiple Shopify stores to 1 Xendit account as you won’t be able to differentiate the order between the stores since the reference ID would be reconciled in the same format on Xendit Dashboard and it’s not editable from Shopify. 

We recommend you to create a new Xendit account to accommodate your other website.

For more information on how to integrate your Xendit account to Shopify, please refer to this article.