I am having a similar problem and it seems like Quickbooks needs to update the process.  I am doing bookkeeping  for a firm and have assigned projects to specific clients.  The firm is renting space, and when the firm receives a bill for rent each month, there is also a charge for copies that were made by the firm.  The copies are chargeable to projects.  When entering the check for payment of the rent and copies, I split the payment into a Rent/Lease Expense and a Client-Related expense.  I assign the appropriate project to the client-related expense, but when I run the project report, the entire amount of the check is charged to the client's project.  I would like for QB to make it so that only the amount for the copies gets charged to the project.  As it stands now, QBO  is creating inaccurate project cost tracking until this is fixed.