Well, first you don't want to send a "digital" signal to the subwoofer. Only analog signals should be hooked up to the sub's RCA connections.
The LFE or subwoofer output on the back of the receiver is an analog signal that is a summed total of ALL bass frequencies for all channels. If you run the R&L signals (receiver pre-outs) to the sub, the sub will combine the signals and only use the bass frequencies from both channels. The R&L outputs from the sub are adjustable so only frequencies above the setpoint will return to the receiver (pre-ins).
Some receivers (even older ProLogic) will allow you to designate the "size" of the front speakers in your system. If you are using the R&L outputs you can set the front right and left speakers as "large". This will make sure all the bass frequencies are sent to those channel RCA pre-outs.