How long exactly is an "overnight" soak of beans, and should I simply add enough cool water to cover them?

It's not hydration that's at issue but rather the cooking temperature.

Some beans, kidney in particular, contain a toxin that requires a hard 10-minute boil to deactivate. Since it's unclear as to which beans contain the toxin and in what amounts, the USDA recommends bringing all types to a boil: See paragraph 11:

http://www.fda.gov/Food/FoodSafety/FoodborneIllness/FoodborneIllnessFoodbornePathogensNaturalToxins/BadBugBook/ucm071092.htm

Most beans should be rehydrated before cooking as some can be poisonous if eatin dry. Eg. red (kidney) beans.

beans absorbed most of the water they are going to take in within four hours. therefore, you can put the beans in water right before going to bed and they will be ready for cooking in the morning. if you are soaking one cup of beans cover it with 1.5 cups of water as the beans will well during the soaking process.
*happy cooking*

I'd say an overnight soak is anything between 6 -10 hours (up to 18?). The time is vague because you can cook beans without soaking them - soaking just softens things and makes for a quicker more gentle cook.

Add a good couple of inches to cover, as they do absorb a fair amount of water during the soaking process.