It appears I am troubleshooting the exact same functionality within the program tonight and had some success.
In my case, the customer prepaid $100 for future services. I received it as Cash under the Cash Accounts tab.
As this was technically Unearned Revenue (a liability) I just made a new account under Liabilities titled Unearned Revenue.
On the Sales Invoice, I added a new line and selected Unearned Revenue as the account and -100 as the unit price.
My tax rates (US Tax Exclusive) were off until I made sure to set the rate specifically for the -$100 line item. Then everything was much closer, but the tax is now overcharging by $0.01.
So while this post is related to invoices and belongs here, I believe it also happens to turn up this issue:
As I am going back and reading this thread now, I am still scratching my head at best practice/expected behavior.