The S1 and S2 pins switch to control the output banks. There are 4 options:
1) The most common use is if the design engineer wants to use it as PLL (zero delay mode).
Set S2 = 1, S1 = 1.
2) They may also be configured to use the CY2309 as a buffer(No zero delay). This mode is used for JTAG testing.
Set S2 = 1 , S1 = 0.
3) If a customer just wants to use bank A and disable bank B to 3-state, then
set S2 = 0 , S1 = 1.
4) If a customer wants to disable both banks to 3-state, then
set S2 =0, S1=0.
The PLL is running in all cases except for case 2. In this case the PLL is powered down to save power since this mode is just like a buffer.
Case 1, your output will be the same as your input with Zero Delay.
Case 2, your output will be the same as your input with NO Zero Delay like a normal buffer.