Books/Square integration with multiple bank accounts

Books/Square integration with multiple bank accounts

Hello,
I need some workaround ideas!

We have two parts of our business which have their own bank accounts and customers. We use 'locations' in Square to allocate the payments to the correct place and we use 'branches' in Zoho Books to define which transactions belong to each, including invoices.

What we need to be able to do is direct all payments for 'Books Branch A' to 'Square Location A' and 'Books Branch B' to 'Square Location B'. This doesn't seem to be possible within the Square/Books integration. 

Can anyone suggest a way that we can connect payments to the correct bank account when a customer clicks the Pay Now link? Whether that would involve coding or just a workaround, I would be grateful for some ideas and to know whether other people have had this issue?

Emma