I currently have one Shopify B2C store and use Xero for my accounting. The Xero app works really well.
I have a second and still developing second Shopify store, B2B as a wholesale branch of the same business.
I want to be able to integrate both of my Shopify stores into the one Xero account (as it is the same business), which at the moment the Shopify made Xero app cannot do.
I have set up all of the backend in Xero to have a separate accounts in the Chart of Accounts and a separate bank payment account to link to Xero so there is no duplication. Essentially the only thing they have in common is the Xero app.
I have spoken to Shopify who said that it is possible, the process is essentially disconnecting one Shopify store from the Xero App and connecting the other store, doing an export and then connecting back to the original store and continuing the process.
Looks like I will be doing this on a weekly basis, but still, I think that it is a bit silly.
Also - I somewhat feel that I would not be the only online merchant to use Shopify and Xero and have two stores.
Does Shopify have something in the pipeline to change this (allow two stores to connect to the one Xero account - provided all the back end is set up like mine)