In general, Lithium-Ion batteries don't like being discharged frequently, and decent computers will cut off the charging circuit once the battery is fully charged.
If I am using it, do I let it discharge, or leave it plugged in?
Leave it plugged in, if your battery is at 100% the circuit is shut off, and you're essentially not using your battery at all, helping its life expectancy.
If I am discharging it / allowing it to be unplugged, should I plug it
in again when it reaches a certain %?
You shouldn't be doing it generally. Batteries only need about one full cycle (full discharge-charge) per month to stay healthy.
Is there a particular battery level I should wait for before shutting
down / recharging?
As stated before, it's recommended to stay at 100% and only run one charge cycle about once a month. This charge cycle can be one-time where you fully discharge/charge it, or it can be several partial cycles (for instance 5 cycles where you discharge to 80% and then charge back to 100%)
When is it okay to close the lid vs. shutting down completely?
It depends. As per question 1, if your computer is plugged in it won't be using the battery at all, so no harm there; but if your computer isn't plugged in, it will consume battery charge (though not much). So if you're going to leave your computer unattended for a considerable time, you want to either leave the computer plugged in, or shut it down, or take advantage of the charge usage as part of your "monthly charge cycle". I'd say its ok to put it in sleep mode unplugged only for short periods of time, such as driving to work/home, but it might even be ok to do so for the night, to force your monthly charge cycle.
Bottom line: battery life expectancy is measured in cycles, so the worst you can do is to constantly discharge and recharge it. Leaving it plugged in helps your battery life by not using it at all.