Avalara Tax and Down Payment Invoices

We use down payment invoices to bill our service agreements, and agreement invoices to create the revenue recognition invoices.  We currently calculate tax on the down payment invoice, and use the "down payment invoice was previously taxed" box so tax is not duplicated on the agreement invoices.  This allows us to send one invoice to our customer that includes any applicable tax.  We also use down payment invoices to charge customer for Deposits so we can collect payments in Advance.  We recently added Avalara to create the tax liability. We were disappointed to find out that Avalara does not create tax on Down payment invoices, but does create the tax on the monthly agreement invoices.  Avalara also disables the "down payment invoice was previously taxed" box, so we can't use that.  Avalara told us that this is a CW issue.  Can an enhancement be created that will allow Avalara to create tax on Down Payment invoices.  Does anyone in the forum accomplish agreement billing in a different way than we are doing it?