Which Subwoofer Connection Should I Use?

My Subwoofer is a Velodyne CT-120 and has L and R speaker wire inputs and outputs, and L and R RCA inputs and outputs (no LFE). My A/V receiver is a Harmon Kardon 240 and has 7 speaker wire outputs (L, R, C, SL, SR, BL, BR) and the same pre-outs plus one for subwoofer.

I was told I can run parallel speaker wire out of the front L and R channels of the receiver and feed those into the L and R speaker wire inputs on the sub. I was also told I can run RCA from the L and R pre-outs on the receiver to the L and R RCA inputs on the sub.

What are the differences sonically, and are there any other options? Which is recommended?
Use the Subwoofer out on the receiver via an RCA cable. For movies you need the LFE channel! This will let you use the processor to change whether you want to run the NHT's full range, roll them off, etc.. you can experiment for both music and movies.. if you use the speaker wire you are severly limited when switching between movies and music setups.

It's never a good idea to run your speaker cable through a sub as the crossovers are cheap and will degrade your main speakers performance..... Plus later if you want to bi-amp your NHT's just pickup a NHT SA3 or SA2 to biamp the bass drivers...

Congrats! Your system is progressing very nicely...

Also make sure to position those NHT's as close to the back wall as posible for the best bass and follow the directions on measuring the distance between and to the listener..... The NHT's are the easiest to setup speaker system I have ever used.. I had some NHT 3.3's.

To get the LFE channel for movies, I have my receiver's subwoofer setting on "no" so it sends the LFE channel to the L and R channels. Then I use the L and R pre-out to go into the subwoofer L and R line inputs.

If I go the route of using the subwoofer out on the receiver, should I use either the L or R input on the subwoofer?
If you use the subwoofer out on the reciever you can choose whether to configure you left and right speakers as large or small and also whether to either rolloff or cut the bass below xxHZ.. these are typical settings for surround receivers.. you manual should cover them but no you shouldn't run the speaker cables into the subwoofer at all.
So it looks like I'll have more control over what gets sent to the subwoofer if I use the subwoofer out, but here is what the choice is down to:

1.) Using the receiver's pre-out L and R into the subwoofer L and R line in with the receiver's "subwoofer" setting on "no" so the bass frequencies get sent to the L and R channels that I'm feeding into the sub.

2.) Using the receivers sub out into the subwoofer L line in.

Technically, the same frequencies should be getting sent to the subwoofer, but in the first case there are two lines going in and in the second there is only one. Which one is better?
2) is better because the $1.50 crossover in the subwoofer is going to make your clean left/right channels muddy... keep your signal path as short and clean as possible.
So when I listen to music in only 2 channels, does the subwoofer still receive a signal?
The cool thing is that with a surround receiver/processor you can choose when you want the subwoofer on and off... some will even let you change the crossover down for music. (aka 40hz for music, 80hz for movies..)