You can enter the first two payments as deposits on the sales order through AR-N.  You can print the sales order with deposits applied if they want a current amount owed.  When the item is shipped and final payment is received, you apply both the payment and the two deposits.

It gets stickier (from an accounting standpoint) because it really is not correct to show revenue without also posting the associated COGS and the 25% upon order placement is prior to incurring any COGS so it really IS a deposit.  The 30% upon release for fabrication may have engineering costs associated with it so it could be tracked and billed as a separate Engineering item using a separate part number and work order to track engineering costs.  Progress billing during actual production gets even trickier because you should relieve the work order of a percentage of COGS as you invoice progress billings.

We do these all the time and have ended up doing manual invoices from Word or Excel.  Upon receipt, we enter their payment as a deposit, which is linked to the sales order.  Then at time of shipment the deposits show up on the invoice.   Seems to work good for us.