PWM (Pulse Width Modulation) is the way that a motherboards bios can control the fan speed according to the temperature. Fan headers and fans with 4 small pins instead of 3 are PWM. You don't have to use it if you don't want to. It's just an option that many people like to use. The advantage of the Y adaptor and hooking both fans up to the same header is they would then be controlled as one unit and would allow the Push/Pull to work more efficiently. If you don't use PWM then just hook each fan up to a separate header.
for more details on PWM Fans.