Pullups are uses as a logic 1.
So to write a 1 to the device being programmed you set the IO pin on the FPGA as HIZ or input, this will allow the Weak pullups to pull the pin to VCCX so putting a logic 1 on the pin.
The point of this is that a logic 1 is always the same as VCCX so if you want to program for example a 2.5V device then as long as VCCX is at 2.5V then the logic 1 will be the same voltage.
If we used the FPGA pin to output a 1 then this would be 3.3v, not good for a 2.5V or 5V or 1.8V device...
Do you understand now?