I guess it depends on what receiver/surround sound processor/PC. Usually, the best way if you have a good sound processor that has great crossovers like the
Outlaw Pre-amp processor: http://www.outlawaudio.com/products/975.html.
In other words, you may not want the sub doing the crossovers but letting the receiver/surround sound processor/PC doing it. In this case, the RCA inputs to the sub and then wires to your speakers from the receiver/surround sound processor. The best way depending on your electronics.
The other option is running the rca to the sub plus the speaker wires to the sub so the sub can crossover everything(it separates the sound frequencies).
This may not be your best option but will work ok.