Wakeup pin is used to bring the FX2LP CPU out of suspend through an external interrupt generating by asserting the pin.
Holding WAKEUP asserted inhibits the EZ-USB chip from suspending. This pin has programmable polarity.
The WAKEUPCS register can be used to enable/disable individual wakeup (WUEN/ WAKEUPCS.0 for Wakeup pin) and set its polarity ( WUPOL ).
If you want the EZ-USB to never go to suspend state, you can leave the pin asserted (low/high) depending on the polarity set in the WAKEUPCS register (WAKEUPCS.4/ WUPOL).
Thanks for the help, I have understood.