Link Estimate to Project

Go to Menu -> Sales -> Estimates and click Create New Estimate

Select customer.

A drop-down with projects will be shown below the customers select field (if no projects associated with the selected customer the dropdown with projects wont be shown)

Select the project

Configure the estimate for your needs

Save the estimate

Navigate to the project area and click on the tab Sales->Estimates you will be able to see the newly created estimate associated with your selected project.