Set it to what you like so long as it's not bottoming the device out. It's as simple as that. I've found the calibration settings to be unreliable. It's either set too hot or too low. I've always had to tweak things afterwards.
There's no right answer. Just play a movie (like Cloverfield) that has some very long, intense bass scenes and adjust to what sounds good to you. Some like it a little hotter than others. Some like it a little subdued. It's all preference.
As for the frequency, you should have the receiver set at 80hz for the LFE crossover. You should have nothing above that being sent assuming your mains can get that low. If you have tower speakers or mains that have decent low end output you might have some overlap that you can dial in on the sub. Again, just use your own ears. You'll hear when the sub is too bloated over the mains. You might have to bump the crossover on the sub down a tiny bit below 80hz.
In most of my setups I've usually had the level on the receiver LFE set at at +1 or +2 and then the gain on the sub is usually around 10 o'clock on the dial. I like it running a little hotter than normal. But sometimes Audessy puts my receiver setting at like -6.
Also make sure you do the "crawl" test to get your sub placed in a good response in regards to your listening position. LFE is *very* sensitive to placement.
