Which security bit option in the Quartus II software should be used to program the security bit in my Altera device?

There are two methods of enabling the Security Bit in the Quartus® II design software for Altera® devices.

1. Checking the "Enable Security bit support" option in the Device and Pin Options dialogue box
2. Checking the Security-bit check box in the Quartus II Programmer

If you enable the security bit support option in the Device and Pin Options in your project and add the corresponding .pof  to the Quartus II Programmer GUI, the security bit check box will automatically be checked.
If you uncheck the check box, then the security bit will not be programmed, even if you enabled the option in Device and Pins Options. In other words, the security bit option is not set in the .pof, you must verify it is enabled in the programmer GUI.