Hi @Andy_B
Firstly, the set up you’re using sounds correct - Braintree would in effect be a bank account, the same as PayPal, Stripe etc.
Secondly, I’m not familiar with Braintree, but hopefully I can offer general guidance. I’m aware Braintree is part of PayPal, so do they offer a running summary of transactions, like PayPal does, e.g. a list of transactions in and out? Or, do they provide a daily or weekly summary at all (e.g. amount collected in that time period, amount paid out in that period)?
I’d be inclined to say this would be the best data to check it against and use the recon tool in the bank account to match it up.
The other thing that may help, is while you’re not able to show the invoices paid from a particular bank account, you can view a list of payments, although not filtered by the bank account it originates from. This can be found by going to Sales >> View payments.
I hope this helps?