I have one company, and 3 branches.  All accounting (including payments) operation will be done at company level.  I have created 3 branches as warehouses with locations.  

1. When I create an invoice and pay through supplier payments, I would like to link with branch (Warehouse).  So that I can see profit or loss at branch level.  

Currently I am not able to link branch with invoice.  

2. I tried with analytic accounting also. However, "chart of analytic accounts" will display all confirmed invoices' numbers, instead of just payments.

It is very simple concept of a company can have 4-5 branches, only the main company will do all financial transactions.  I am missing some configuration, please correct me.