Can I invoice in stages?

Yes.

• In Engineering Consultancy: add the project stages with their percentage or amount (design 30%, drawings 40%, supervision 30%…). When a stage is done, add an invoice of type Works invoice (stage) and pick the stage; it goes to ZATCA for that stage's amount alone. Projects billed by period use payment certificates.
• In ordinary invoices: issue a separate invoice for each agreed payment or stage.

Each stage's VAT is then due only when it is done.