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

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.