I am bumping this question up as I have the same issue within QBO. 

I  need to include an expense on an invoice; the reasoning is that in the trucking industry, the "customers" provide fuel to the truckers and they deduct the fuel on the truckers pay.  That fuel has to be recorded as an expenses and the ITC needs to be tracked and reported on the period HST remittances.  

I fail to see how to do such a transaction in QBO without netting the HST between the income and the expense (which is a big NO with CRA). 

Example :
Client hauled for 15,000 + HST and was deducted 2,250 for fuel + HST

The entry should look like

A/R                       DT  14,.407.50

Fuel Expense      DT 2,250.00

HST ON Purch    DT 292.50

Sales                                            CT  15,000.00

HST on Sales                              CT 1,950.00

QBO will only do the following (unless I am mistaken) which is wrong.

A/R                       DT  14,407.50

Fuel Expense      DT 2,250.00

Sales                                            CT  15,000.00

HST on Sales                              CT 1,657.50

This is ultimately a single transaction that needs to go through the sales module as my client needs to track the HST on sales, HST on purchases and will also be receiving the net amount, so I can't enter an sales invoices and a bill to pay.