I am having similar issues.

We use projects and create parent companies.  So when we have a parent company call with a job, we create a project for that specific location.  When we invoice out, we invoice under each project.  Problem is when the parent company pays, they send us authorization to process a single credit card transaction for multiple invoices.  I can not accept a credit card payment for more than one invoice at a time.  It should be set up so that, under a parent account, multiple invoices should be able to be processed in one transaction.  

I've yet to figure it out.