Best way to hook up a sub?

Is this for a home theater or a hifi system?

If it's for HT, it's easy enough to hook it up. Just use the LFE output from the AV receiver or prepro.

For music, it's a bit more difficult. You might want to look at one of these boxes:

http://velodyne.com/product-accessories/management-systems/sms-1-digitalmanagement-system.html

It's always a bit difficult to integrate a subwoofer with main speakers. One thing I try not to do is to muck with the main speaker's crossovers. The speaker designers have put a lot of work into the speakers' internal crossovers so adding another crossover stage in front of it is going to muck it up further.

Something like the Velodyne helps you adjust the subs output to make sure it complements the main speakers by augmenting what it can't fill rather than using a separate crossover in front of the main speakers.

I'm not a big fan of adding another crossover in front of the speaker's crossover.

Try downloading the Thiel SmartSub manual. There's a section on subwoofer placement.

I think centre between the 2 speakers is best for a single sub

Having corner reinforcement increases the output but I think it also can be muddy and not be as tight.

I remember before Audyssey AutoEQ for HT, I used a Behringer DEQ2496 to tune the subwoofer. A good flat response from the subwoofer sounded "less" to me but after a while, you realize you get more low level information than before.

I liked having my single sub between the mains because it doesnt seem as directional. Now I run it in stereo.

ps if you can, you can push the sub against the wall (but still between the speakers) to increase the output a bit.