"They then collect a 60% deposit prior to starting the project. I know I
can set up a liability and create deposit invoices, or the better way
is to use progress invoices."
Not for a Deposit or prepayment. The deposit is not against the Scope of work, but the anticipation that we agree to this scope and want some Assurance of the true commitment = pay us a bit in advance.
"Most of our contractors want to see one
invoice, with 60% of each estimate."
Customers?
"Progress invoicing allows you to
create a 60% invoice per estimate, but how can I do this for multiple on
one invoice? And, will it show each item at 60% or just one line of
60% per estimate?"
You make one Other Charge Type item for Prepayments. Link it to Liability, if you are allowed to carry it as Liability. Otherwise, it is linked to Income.
Use it on an invoice to "request" the payment; or, on a Sales Receipt, because the Contract terms already resulted in the inclusion of the Prepayment when they returned the signed contract.
Use it again, later, as you Progress Invoice for Scope completion. You are creating a Credit Memo for that job with that item for the amount to use in lieu of More Money being sent. For instance:
I request 10% of the contract up front.
I apply half to your First invoice from the work performed. I apply the other half to the Final invoice for the project. That means the credit memos are dated for the invoices I want to apply the prepayment against, to show how I used up your prepaid amount.