You can wakeup from DeepSleep mode periodically by using the WDT (WatchDog Timer) and the LFCLK (Low Frequency CLock). When you have got an external signal to wakeup the chip you may connect that to a pin and get woken by an interrupt. There are only few components running in DeepSleep.
These might help -
http://www.cypress.com/documentation/application-notes/an86233-psoc-4-low-power-modes-and-power-reduction-techniques AN86233 - PSoC® 4 Low-Power Modes and Power Reduction Techniques
http://www.cypress.com/documentation/application-notes/an90114-psoc-4000-family-low-power-system-design-techniques AN90114 - PSoC® 4000 Family Low-Power System Design Techniques
http://www.cypress.com/documentation/application-notes/an92584-designing-low-power-and-estimating-battery-life-ble AN92584 - Designing for Low Power and Estimating Battery Life for BLE Applications
How can I close ECO clock in my lowpower mode? Use CysysclkEcoStop() API or disable ECO component in .cysch ? I found CysysClkEcoStop() is useless when I was testing my deep sleep mode current consumption, but disable ECO component in .cysch is useful, it made my current consumption smaller.
In AN92584 did you implement the BL:ESS power mode before turning off ECO ?