There is no right one way to setting up a subwoofer system, but there are some common denominators. The first is as @erik_squires described, a complete two way crossover is mandatory preferably digital because this is the only way to accurately time align the individual drivers. @james633 With a 64 bit floating point processor running at 24/192, DSP is totally invisible. There are only sonic advantages and no disadvantages as long as good DACs are being used.
The most important concept that Geddes advances is the use of multiple subs also championed by @audiokinesis. Two is the minimum, I use 4 as does audiokinesis.
@audioquest4life It is not the size of the woofer that counts, it is the frequency range it operates in. The higher a woofer goes the more important is the use of a high pass filter. Many large woofers are running up to 350 or even 500 Hz. This is well into the midrange. Middle C is 256 Hz. Bass under 100 Hz will cause doppler distortion of everything else carried by the driver. The is also no such thing as too much head room. You also have to use a filter if you plan on time aligning the drivers which IMHO is mandatory.
Another important concept is running low bass with up to 20 dB of gain. This gives you the visceral character of a live performance. If done right it does not make the bass warm or boomy it just increases the vibratory sensation of the music. My favorite curve increases bass at 4-5 dB/oct from 100 Hz down. 20 Hz is hot by 10 dB. Some rooms may require more.
The room is key. I am very fortunate as my listening room was designed as such and there is no back wall. The room opens to the rest of the floor which is acting as one big diffusor. So in my situation I am listening just as much to the drivers as I am to the room whereas most people are listening more to the room.
Another important factor that was mentioned was room treatments for bass do not work. It is a total waste of money which could have been spent on another subwoofer or a better crossover.
@erik_squires I have no idea in this day and age why someone would use a ported loudspeaker. We have loads of powerful amplifiers and digital signal processing can give you any reasonable frequency response you require. Subwoofers in particular should always be sealed as port noise is ubiquitous with the amount of air moved by a subwoofer driver. The effect of lowering many types of distortion including IM, Harmonic and Doppler and increasing headroom is just as important as adding low bass when using subwoofers with two way crossovers. Good for you. Now try getting this into the heads of most subwoofer users who are being sold a bunch of malarkey by the manufacturers.