Stage payments are instalments paid as defined milestones are completed and certified, rather than a lump sum at the end. They keep the builder funded while ensuring you never pay significantly ahead of the value of work in place.
The golden rule is to pay for work done, not work promised. Each stage should be defined in the contract by an objective, inspectable milestone, and payment should follow a certificate from your architect, engineer or surveyor.
Retention of a small percentage of each payment, released partly at practical completion and partly at the end of the defects period, gives you leverage to have snags fixed.