"Receive Payment", "Class" & "Estimate"

I have a couple of questions:

(1) We utilize QBO's default "Unapplied Cash Payment Income" account to document individual client's "credit/retainer on file" for a various reasons.  Because of this, we void Sales Receipt when one is automatically created by QBO upon client's payment via Payment Link.  We then utilize "Receive Payment" function to match the payment to actual deposit.  Sales Receipt has a field for Class, but Receive Payment does not.  Is there a way to assign a class to payment, so when we send a Class report to our client, the report can capture their total amounts paid?

(2) We tried using the "Deposit" field in individual invoice to reflect the retainer received.  However, (1) I am unable to choose the retainer's Current Liability account to offset the deposit, and (2) when I tried to apply the deposit, it not only lowers the overall amount due on the invoice (which is correct), but it also lowers the amount associated to the related estimate.

For example:  We have an estimate of $1,000 for a job. Client has paid a retainer of $500.  This month, an invoice for $100 is generated.  When I apply the retainer of $100, it lowers the overall invoiced amount to $0.  This is correct.  However, with a progressive invoice, the detailed information related to the linked estimate (shown at the bottom of the invoice) would show the estimate of $1,000, and this invoice is $0, which means the overall estimate is still $1,000 while technically, the overall estimate has been reduced by $100 invoiced.  Is there any way for the invoice to accurately reflect its association to both estimate and payment?

I appreciate your help!

Michelle