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I had this same problem, and couldn't find the answer anywhere. This might be a recent addition to Quickbooks, but I stumbled on it.
Edit > Preferences > Jobs & Estimates > Company Preferences > "Do you do progress invoicing?" - YES
Instead of an Invoice, I would create a Sales Order or Quote for $50.00 + applicable tax, requesting 50% Deposit (or $25.00) These are both Non-Posting transactions that don't affect your finances.
When you receive the $25, use the Receive Payments to record it. This will create a Credit in the Customer's account.
When you fill the order, turn the Sales Order into an Invoice with the current date and apply the $25 Credit, The balance owing will be $25 + Tax on $50.00. Your Sales and Taxes are now both accurate.
Here's an article that I refer to when I receive deposits on jobs that haven't been invoiced yet. You can state the terms in the body of the Sales Receipt. Maybe this will help you too.
We started using this progress billing option, but I hate that it breaks up the item quantity not just the dollar value, so we end up with half items in inventory which I really hate. Even though it shakes out after the final invoice, it just looks messy. I find this silly. Anyone find how to stop this?
Do you know how I can insert on all my invoice a down payment of 30% ? So the clients will know what he has to pay to statrt the job.