What is te absolute best way to hook up a sub?

There are so many variables, your question cannot be answered with the information provided.

First, what subwoofer are we talking about? What are the other components? What is the listening room like (carpet, hardwood, concrete basement, new, old house, etc)?

Even things like room placement matters regardless of everything else...

Jon, it really depends on the sub. The stereo inputs on the amp of most subs are wired together just inside the box anyway, so only one cable w/o the Y-connector is needed. Some subs like mine (Art of Sound) and REL connect to both the LFE input and at the same time to the speaker taps from my receiver ( R/L positive, L negative) with a SPEAKON connector. i also have two gain adjustment knobs. Some subs could be connected from the R/L pre-outs to the sub and back to the processor. This mens you're sending a full range R/L signal to the sub first , then back to the processor then out to the R/L speakers. This will allow for a decent blend for music but how it blends w/the other speakers for HT may be different. Just a few experiences I've had. Hopefully, you'll get more suggestions.

There is NO ABSOLUTE way to hook up a sub.

There is NO absolute bestway to hook up a sub.

And absolutely, two subs are better than one.