We do this on a regular basis when requiring a down payment for a large order or because of a similar credit issue. We created a miscellaneous item code (/Downpayment) that is added to the invoice. All the sales order items are listed with a shipped quantity of zero. Then when shipped and the final invoice is generated, simply add the downpayment code again as a negative to correctly reflect the balance due.

I should add that the misc. item code is linked to a customer down payment liability account so that no revenue is recognized until the items are shipped and invoiced.

You don't need to list the cost, you are just taking a deposit on the order. Just create a Performa invoice out of a sales order form and print it out.  When the money comes in just enter the check number on the totals page and enter the amount. The balance will show up.

How does one enter/create a pro-forma invoice in Sage 100 (2018)?

Create a new sales order form code and edit the Order Title formula.  Here is ours. Note that if the order is a Quote or Sales Order it says Proforma Invoice.

select case {SO_SalesOrderWrk.OrderType}
    case "S"
        formula = "Proforma Invoice"
    case "B"
        formula = "Proforma Invoice"
    case "M"
        formula = "Master Order"
    case "R"
        formula = "Repeating Order"
    case "Q", "P"
        formula = "Proforma Invoice"
end select

That is the approach we want to take.  However, I cannot figure out how the deposit is flowing into the correct GL account.  The account is set up in the GL and in SO Options but nothing is showing up in that GL account. So where is the deposit recorded or what am I doing wrong?