No, you normally don’t have to re-apply for both stages. Some people prefer to get the Global Talent visa (ex Tier 1 Exceptional Talent visa) for 1 or 2 years initially even if their endorsement covers 3 or 5 years. When the 1-year period finishes, you can extend your visa by submitting the documents for Stage 2 bypassing Stage 1. Learn more about extending your visa here.