Speaker level inputs typically insert about a 100uF electrolytic cap into the signal path which may be the worst possible way to add a high pass filter and will affect the signal to the main speakers. But as always, it's your choice.
Does not apply in the case of our method of integration for the Blumenstein Audio Dungeness subwoofer.
For speaker wire hookup, the lengths of speaker wire used for the subwoofer amplifier's inputs is simply doubled up (biwired) at either the binding posts of the fullrange speaker or alternatively at the binding posts of your stereo amplifier. Either place does not affect the sound quality. As well, it can be an assymetric hookup location in this respect without affecting sound quality, which is convenient as well.
The quality of this speaker wire is essentially inaudible as well, which is also convinient because the quality of the typically long length of RCA cable for the inputs would be audible. I recommend cheap high gauge wire that comes on a roll. This set of speaker wires only goes into the "from amplifier" section of inputs of the subwoofer amp, (and does not come back out of the "to speaker" outputs, which keeps those nasty electrolytic caps from being engaged). Its a pure and simple method of hookup, and only bleeds a tiny amount of signal from a Power Amp, rather than drawing 50% of the output of a Pre Amp.
RCA hookups can have some sonic advantages in certain cases, however, and in the case of Bottlehead products, RCA subwoofer inputs work very well! So in general, I feel that speaker level vs. RCA hookups for a subwoofer will all depend on the makeup of the rest of your system. While speaker wire inputs are universally compatible for prettymuch any power amplifer, some Bottlehead Pre-amps have a provision for dual RCA outputs ((one set to the stereo power amp, one set to the subwoofer(s). And they sound great hooked up that way with my speakers/subs! I like to match lengths (a less practical recommendation) and types/brands (a more practical recommendation) for the quad of RCA cables coming from the back of the pre amp.
Hope those explainations and tips help!
Best,
Clark