Before diving into subwoofer placement and optimization, you need to understand the basic terminology. This is more than just background; it will help you isolate problems with your subs, and even spur you on toward considering building your own sub one day.
More often than not, home theater consumers think of a subwoofer as just another speaker. Although that might be true in some senses, you're better off considering subs as a completely different category. This perspective dovetails with the very nomenclature of the system; it's not a six-channel system, it's a 5.1 system (with the subwoofer being the ".1"). You need to consider different factors when choosing a sub, but first, let's get some basic terms under your belt.
The first thing to get into your head is the actual part list, so to speak, of a typical subwoofer.
A subwoofer is a speaker specialized for producing bass (usually frequencies below about 120 Hz). They can be active (where a plate amp is built into the enclosure) or passive (requiring a separate amp). A subwoofer is made up of an enclosure, a driver, and, if it is active, an amplifier.
A plate amp is an amplifier built on a plate that can easily be mounted to a subwoofer enclosure. It can have speaker-level and/or line-level inputs, and possibly outputs. It can have one crossover or no crossover, as well as rumble filters, phase controls, and an EQ (equalizer).
A driver is the part of a subwoofer (or ...