I assume you are using old CapSense component. We recommend you to use CapSense V6.0 for better performance.
Pls refer to Section 5 of http://www.cypress.com/file/46081/download for information on different tuning methods.
CapSense initialization and calibration occurs during CapSense_Start() API.
To know the time the component takes to initialize, you can toggle a GPIO before and after the API is called. The time differs for different CapSense component configurations.
I hope this helps.