Almost 3 years since your question, but I've found an answer that works in Quick Books Online. I have not tested it in the Desktop version.

My conjecture was that using an invoice was causing Quickbooks to classify the transaction under "Sales". So the first step was to use journal entries -- first between A/P and a liability account "Customer Advance Payments"; then, when the customer pays, between A/P and a bank account. Unfortunately, this still resulted in the advance payment showing up in "Sales".

So then I looked at the journal entries to see if anything could be causing them to be considered "Sales". Sure enough, I had put "Exempt (Sales)" in the Sales Tax field. When I deleted this (the "Sales Tax" field is now empty) and hit "Save", the transaction magically disappeared from "Sales".

When you use a Sales Invoice in QBO, the Sales Tax field cannot be left blank. So using journal entries is the only workaround for this bug in QBO. It may be different in Desktop.