Down Payment Invoice and Credit Memo

We are a software company selling licenses and related consulting services. We charge customers based on billing milestones on our contracts. For example, we can put 50% of licenses and services upon signing the contract and 50% upon project completion. Our first billing is purely for customer deposit purpose since we have not deliver anything yet. Rev rec is controlled by Rev Rec Commit based on project percentage every period. My question is how I am able to create an invoice to collect payment on Sales Order level. I know I can create payment on to Sales Orders and create