Let me help share information about how QuickBooks calculate the amount of each invoice when utilizing progress invoicing.
You're on the right track. Even if you've invoiced your customer 50% for the first month and 20% on the second, it'll still calculate 70% as the invoiced amount since the original estimate has not been closed from where they were linked into.
With this, you can consider creating a separate progress invoicing if you wish to create 20% amount of transaction after creating the other one with 50% of each line item.
Learn more about how progress invoicing works with this article: Set up and send progress invoices in QuickBooks Online.
Additionally, I've got you this helpful article for ideas about the different methods you can start using in accepting payments from your customers: Record invoice payments in QuickBooks Online.
Stay safe and comment below or post again if you have any other questions. I'll be here to lend a hand.