Setting up a worker pool within Spacelift involves generating a worker private key, creating an AWS Cloud Integration, obtaining Spacelift's mothership IPS, and setting up a network. After these steps are completed, the user can create a worker pool in their Spacelift account by providing necessary details such as name, uploading spacelift.csr file, selecting a space, and attaching cloud integration. The final step involves running an automation to generate workers within the created worker pool.