The unfiltered input is the one you'd want to use if you are connecting the sub to the receiver's sub pre-out. You'd set the crossover frequency for directing the bass from the other speakers to the sub in the receiver's setup menu. This is the normal and preferred way to hook up the sub if you are using it for home theater.
You do not need a Y splitter, although using one will not hurt anything. Feeding both left and right low-level inputs will increase the signal level very slightly but not enough that you'll really notice.
The sub has multiple inputs, including the speaker level ('high level') inputs, for flexibility so that the sub can be used in many different setups. If you were to use the speaker level inputs or the filtered low-level inputs (that you connect to with a single 75-ohm cable with an RCA plug on the end or use a Y to connect both the left and right), then the sub would be doing the crossover functions and you set the xover frequency using the xover dial on the sub (it might be labeled 'low pass' filter).
Use a single RCA cable from the receiver's sub pre-out to the subwoofer's unfiltered LFE input and you're all set.