The BOSE system is definitely better than the basic factory setup. It offers an amplifier (more power/clarity), better speakers (2-way coaxials with reasonable woofer/tweeter combination), and a small sub, and appropriate crossover filters so that the speakers don't prematurely distort from too much bass.
An aftermarket system is usually better again, subject to quality and installation.
You're not quite comparing apples with apples: adding a subwoofer to the basic factory system (ie: with factory speakers, no amplifier) vs a complete BOSE system. However, the FLi sub should easily outperform the BOSE version, but you'll still have pretty poor speakers that have no hope of keeping up.
You can connect it up via high level audio inputs to the amplifier; if it doesn't have direct high level inputs, you'll need a line output converter. You'll also need to install appropriate powerwiring, fused, directly from the battery. Given your question, I suspect you'll need it professionally installed.